Tinker User's Guide

TinkerTools Organization

Apr 07, 2025

 CONTENTS

1 Introduction to the Software 1

1.1 What is Tinker? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Features and Capabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.3 Contact Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

2 Installation on Your Computer 5

2.1 How to Obtain a Copy of Tinker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.2 Prebuilt Tinker Executables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.3 Building your Own Executables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.4 Tinker-FFE (Force Field Explorer) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.5 Documentation and Other Information . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.6 Where to Direct Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

3 Types of Input & Output Files 9

4 Potential Energy Programs 13

5 Analysis & Utility Programs & Scripts 21

6 Force Field Parameter Sets 27

7 Special Features & Methods 41

7.1 File Version Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
7.2 Command Line Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
7.3 Use on Windows Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
7.4 Use on MacOS Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
7.5 Atom Types vs. Atom Classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
7.6 Calculations on Partial Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
7.7 Metal Complexes and Hypervalent Species . . . . . . . . . . . . . . . . . . . . . . . 44
7.8 Neighbor Methods for Nonbonded Terms . . . . . . . . . . . . . . . . . . . . . . . . 45
7.9 Periodic Boundary Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
7.10 Distance Cutoffs for Energy Functions . . . . . . . . . . . . . . . . . . . . . . . . . . 45
7.11 Ewald Summations Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
7.12 Continuum Solvation Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
7.13 Polarizable Multipole Electrostatics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
7.14 Potential Energy Smoothing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

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 7.15 Distance Geometry Metrization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

8 Use of the Keyword Control File 49

8.1 Using Keywords to Control Tinker Calculations . . . . . . . . . . . . . . . . . . . . . 49
8.2 Keywords Grouped by Functionality . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
8.3 Description of Individual Keywords . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

9 Routines & Functions 107

10 Modules & Global Variables 199

11 Test Cases & Examples 247

12 Benchmark Results 251

12.1 Calmodulin Energy Evaluation (Serial) . . . . . . . . . . . . . . . . . . . . . . . . . 251
12.2 Crambin Crystal Energy Evaluation (Serial) . . . . . . . . . . . . . . . . . . . . . . . 251
12.3 Crambin Normal Mode Calculation (Serial) . . . . . . . . . . . . . . . . . . . . . . . 252
12.4 Water Box Molecular Dynamics using TIP3P (Serial) . . . . . . . . . . . . . . . . . . 252
12.5 Water Box Molecular Dynamics using AMOEBA (Serial) . . . . . . . . . . . . . . . . 252
12.6 MD on DHFR in Water using CHARMM (OpenMP Parallel) . . . . . . . . . . . . . . 252
12.7 MD on DHFR in Water using AMOEBA (OpenMP Parallel) . . . . . . . . . . . . . . . 253
12.8 MD on COX-2 in Water using OPLS-AA (OpenMP Parallel) . . . . . . . . . . . . . . . 254
12.9 MD on COX-2 in Water using AMOEBA (OpenMP Parallel) . . . . . . . . . . . . . . . 254

13 Acknowledgments 257

14 References 261
14.1 Molecular Mechanics & Dynamics Software Packages . . . . . . . . . . . . . . . . . . 261
14.2 Literature References by Topic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267

Index 281

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 CHAPTER

ONE

INTRODUCTION TO THE SOFTWARE

1.1 What is Tinker?

Welcome to the Tinker molecular modeling package! Tinker is designed to be an easily used and
flexible system of programs and routines for molecular mechanics and dynamics as well as other
energy-based and structural manipulation calculations. It is intended to be modular enough to
enable development of new computational methods and efficient enough to meet most production
calculation needs. Rather than incorporating all the functionality in one monolithic program, Tin-
ker provides a set of relatively small programs that interoperate to perform complex computations.
New programs can be easily added by modelers with only limited programming experience.

1.2 Features and Capabilities

The series of major programs included in the distribution system perform the following core tasks:
(1) building protein and nucleic acid models from sequence
(2) energy minimization and structural optimization
(3) analysis of energy distribution within a structure
(4) molecular dynamics and stochastic dynamics
(5) simulated annealing with a choice of cooling schedules
(6) normal modes and vibrational frequencies
(7) conformational search and global optimization
(8) transition state location and conformational pathways
(9) fitting of energy parameters to crystal data
(10) distance geometry with pairwise metrization
(11) molecular surface areas, volumes and their gradients
(12) free energy changes for structural mutations
(13) advanced algorithms based on potential smoothing

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Tinker User's Guide

Many of the various energy minimization and molecular dynamics computations can be performed
on full or partial structures, over Cartesian, internal or rigid body coordinates, and including a
variety of boundary conditions and crystal cell types. Other programs are available to generate
timing data and allow checking of potential function derivatives for coding errors. Special features
are available to facilitate input and output of protein and nucleic acid structures. However, the basic
core routines have no knowledge of biopolymer structure and can be used for general molecular
systems.
Due to its emphasis on ease of modification, Tinker differs from many other currently available
molecular modeling packages in that the user is expected to be willing to write simple “front-end”
programs and make some alterations at the source code level. The main programs provided should
be considered as templates for the users to change according to their wishes. All subroutines are
internally documented and structured programming practices are adhered to throughout. The
result, it is hoped, will be a calculational system which can be tailored to local needs and desires.
The core Tinker system consists of over 240,000 lines of source written entirely in a portable Fortran
superset. Use is made of only some very common extensions that aid in writing highly structured
code. The current version of the package has been ported to a wide range of computers with no or
extremely minimal changes. Tested systems include: Ubuntu, CentOS and Red Hat Linux, Microsoft
Windows 10 and earlier, Apple MacOS, and various older Unix-based workstations under vendor
supplied Unix. At present, our new code is written on various Linux platforms, and occasionally
tested for compatibility on various of the other machine and OS combinations listed above. At
present, our primary source code development efforts are in Fortran, using a portable subset of
Fortran90 with some common extensions. A machine-translated C version of Tinker is currently
available, and a hand-translated optimized C version of a previous Tinker release is available for
inspection. Conversion to C or C++ is under consideration, but not being actively pursued at this
time.
The basic design of the energy function engine used by the Tinker system allows usage of several
different parameter sets. At present we are distributing parameters that implement several Am-
ber and CHARMM potentials, MM2, MM3, OPLS-UA, OPLS-AA, MMFF, Liam Dang’s polarizable
potentials, and our own AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Appli-
cations), AMOEBA+, and HIPPO (Hydrogen-like Intermolecular Polarizable Potential) force fields.
In most cases, the source code separates the geometric manipulations needed for energy derivatives
from the actual form of the energy function itself. Several other literature parameter sets are be-
ing considered for possible future development (later versions of CHARMM and Amber, as well as
GROMOS, ENCAD, MM4, UFF, etc.), and many of the alternative potential function forms reported
in the literature can be implemented directly or after minor code changes.
Much of the software in the Tinker package has been heavily used and well tested, but some mod-
ules are still in a fairly early stage of development. Further work on the Tinker system is planned
in three main areas: (1) extension and improvement of the potential energy parameters includ-
ing additional parameterization and testing of our polarizable multipole AMOEBA force field, (2)
coding of new computational algorithms including additional methods for free energy determina-
tion, torsional Monte Carlo and molecular dynamics sampling, advanced methods for long range
interactions, better transition state location, and further application of the potential smoothing
paradigm, and (3) further development of Force Field Explorer, a Java-based GUI front-end to the
Tinker programs that provides for calculation setup, launch and control as well as basic molecular
visualization.

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1.3 Contact Information

Questions and comments regarding the Tinker package, including suggestions for improvements
and changes should be made to the author:
Professor Jay William Ponder Department of Chemistry, Box 1134 Washington Univer-
sity in Saint Louis One Brookings Hall Saint Louis, MO 63130 U.S.A.
office: Louderman Hall, Room 453 phone: (314) 935-4275 fax: (314) 935-4481 email:
[email protected]
In addition, an Internet web site containing an online version of this User’s Guide, the most re-
cent distribution version of the full Tinker package and other useful information can be found
at https://dasher.wustl.edu/tinker/, the Home Page for the Tinker Molecular Modeling Pack-
age. Tinker and related software packages are also available from GitHub at the site https:
//github.com/TinkerTools/Tinker.git/.

1.3. Contact Information 3

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4 Chapter 1. Introduction to the Software

 CHAPTER

TWO

INSTALLATION ON YOUR COMPUTER

2.1 How to Obtain a Copy of Tinker

The Tinker package is distributed on the Internet at the Ponder lab’s Tinker web site located at https:
//dasher.wustl.edu/tinker/, or via download from the Github site for the TinkerTools organization
at https://github.com/TinkerTools/Tinker/. After unpacking the distribution, you can build a set
of Tinker executables on almost any machine with a Fortran compiler. Makefiles, a CMakeLists.txt
file for cmake, as well as standalone scripts to compile, build object libraries, and link executables
on a wide variety of machine-CPU-operating system combinations are provided.

2.2 Prebuilt Tinker Executables

Pre-built Tinker executables for Linux, MacOS, and Windows are also available for download from
the sites mentioned above. They should run on most recent vintage machines using the above
operating systems, and can handle a maximum of 1 million atoms provided sufficient memory is
available. The Linux executables require at least glibc-2.6 or later. Note starting with Tinker 8, we
no longer provide pre-built executables for any 32-bit operating systems.
The provided executables are OpenMP capable, but do not support APBS or the Tinker-FFE in-
terface. You will still need to have a copy of the complete Tinker distribution as it contains the
parameter sets, examples, benchmarks, test files and documentation required to use the package.

2.3 Building your Own Executables

The compilation and building of the Tinker executables should be easy for most of the common
Linux, MacOS and Windows computers. We provide in the /make area of the distribution a Make-
file that with minor modification can be used to build Tinker on any of these machines. As an alter-
native to Makefiles, we also provide machine-specific directories with three separate shell scripts to
compile the source, build an object library, and link binary executables.
The first step in building Tinker using the script files is to run the appropriate compile.make script
for your operating system and compiler version. Next you must use a library.make script to create
an archive of object code modules. Finally, run a link.make script to produce the complete set of
Tinker executables. The executables can be renamed and moved to wherever you like by editing

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and running the “rename” script. These steps will produce executables that can run from the
command line, but without the capability to interact with the FFE GUI. Building FFE-enabled Tinker
executables involves replacing the sockets.f source file with sockets.c, and included the object from
the C code in the Tinker object library. Then executables must be linked against Java libraries in
addition to the usual resources. Sample compgui.make and linkgui.make scripts are provided for
systems capable of building GUI-enabled executables.
Regardless of your target machine, only a few small pieces of code can possibly require attention
prior to building. The most common source alterations are to the master array dimensions found
in the source file sizes.f. The basic limit is on the number of atoms allowed, “maxatm”. This
parameter can be set to 1000000 or more on most workstations. Personal computers with minimal
memory may need a lower limit, depending on available memory, swap space and other resources.
A description of the other parameter values is contained in the header of the file.

2.4 Tinker-FFE (Force Field Explorer)

Tinker-FFE, formerly Force Field Explorer, is a Java-based GUI for the Tinker package. It provides
visualization for Tinker molecule files, as well as launching of Tinker calculations from a graphical
interface. Tinker-FFE for Linux, MacOS and Windows can be downloaded from the Ponder lab
Tinker web site as “installation kits” containing the FFE GUI and an FFE-enabled version of Tinker.
Tinker-FFE requires a 64-bit CPU and operating system, as 32-bit systems are no longer supported.
Integration with Tinker, including the ability to interactively run Tinker calculations, and to access
molecule downloads from the PubChem, NCI and PDB databases make Tinker-FFE a useful tool in
classroom teaching environments. For research work, we recommend using the latest command
line version of Tinker for numerical calculations, and using FFE or another visualization program
to view results. Several other visualization programs (including VMD, Avogadro, Jmol, MOLDEN,
WebMO, some PyMOL versions, etc.) can display Tinker structure and MD trajectory files.
The Tinker-FFE Installer for Linux is provided as a gzipped shell script. Uncompress the the .gz
archive to produce an .sh script, and then run the script. The script must have the “executable”
attribute, set via “chmod +x installer-file-name.sh”, prior to being run.
The Tinker-FFE Installer for MacOS is provided as a .dmg disk image file. Double-click on the file
to run the installer. MacOS 10.8 and later contains a security feature called Gatekeeper that keeps
applications not obtained via the App Store or Apple-approved developers from being opened.
Gatekeeper is enabled by default, and may result in the (incorrect!) error message: “Tinker-FFE
Installer.app is damaged and can’t be opened.” To turn off Gatekeeper, go to the panel System
Preferences > Security & Privacy > General, and set “Allow apps downloaded from:” to “Anywhere”.
This will require an Administrator account, and must be done before invoking the FFE installer.
Once FFE is installed and launched for the first time, you can return the System Preference to
its prior value. On Sierra (10.12) and later, the “Anywhere” option has been removed. In most
cases the Security & Privacy panel will open and permit the user to run the installer. Alternatively,
the “Anywhere” option can be restored by running the command “sudo spctl –master-disable” in a
Terminal window.
The Tinker-FFE Installer for Windows is provided as a zipped executable. First, unzip the .zip
file, then run the resulting executable .exe file. In order to perform minimizations or molecular
dynamics from within FFE, some environment variables and symbolic links must be set prior to

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using the program. A batch file named “FFESetupWin.bat” is installed in the main Tinker-FFE
directory, which by default resides in the user’s home directory. To complete the setup of FFE,
this batch file should be run from a Command Prompt window following installation. It is only
necessary to invoke this batch file once, as the settings should persist between logins.
For those wishing to modify the FFE GUI or build a version from source, we provide a complete
development package for Tinker-FFE. This is a large download which contains the code for all
components, including the Java source for FFE itself and the many required Java libraries. This
package allows building Tinker-FFE on all three supported operating systems from a common code
base. External requirements are the GNU compiler suite with gcc, g++ and gfortran (on Windows
use MinGW-w64 compilers under Cygwin), and the Install4j Java installer builder. Note Install4j is
a commercial product; only the compiler is needed, not the full Install4j GUI interface.

2.5 Documentation and Other Information

The documentation for the Tinker programs, including the guide you are currently reading, is
located in the /doc subdirectory of the distribution. The documentation was prepared using the
Sphinx documentation generator. Portable versions of the documentation are provided as PDF
files and in HTML format for web display. Please read and return by mail the Tinker license.
In particular, we note that Tinker is not an Open Source package as users are prohibited from
redistribution of original or modified Tinker source code or binaries to other parties. While our
intent is to distribute the Tinker code to anyone who wants it, the Ponder Lab would keep track of
researchers using the package. The returned license forms also help us justify further development
of Tinker. When new modules and capabilities become available, and when the inevitable bugs are
uncovered, we will attempt to notify those who have returned a license form. Finally, we remind
you that this software is copyrighted, and ask that it not be redistributed in any form.

2.6 Where to Direct Questions

Specific questions about the building or use of the Tinker package should be directed to pon-
[email protected]. Tinker related questions or comments of more general interest can be
posted on Twitter @TINKERtoolsMD. The Tinker developers monitor this account and will respond
to the site or the individual poster as appropriate.

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8 Chapter 2. Installation on Your Computer

 CHAPTER

THREE

TYPES OF INPUT & OUTPUT FILES

This section describes the basic file types used by the Tinker package. Let’s say you wish to perform
a calculation on a particular small organic molecule. Assume that the file name chosen for our
input and output files is sample. Then all of the Tinker files will reside on the computer under the
name sample.xxx where .xxx is any of the several extension types to be described below.
SAMPLE.XYZ
The .xyz file is the basic Tinker Cartesian coordinates file type. It contains a title line followed
by one line for each atom in the structure. Each line contains: the sequential number within the
structure, an atomic symbol or name, X-, Y-, and Z-coordinates, the force field atom type number
of the atom, and a list of the atoms connected to the current atom. Except for programs whose
basic operation is in torsional space, all Tinker calculations are done from some version of the .xyz
format.
SAMPLE.INT
The .int file contains an internal coordinates representation of the molecular structure. It consists
of a title line followed by one line for each atom in the structure. Each line contains: the sequential
number within the structure, an atomic symbol or name, the force field atom type number of the
atom, and internal coordinates in the usual Z-matrix format. For each atom the internal coordinates
consist of a distance to some previously defined atom, and either two bond angles or a bond angle
and a dihedral angle to previous atoms. The length, angle and dihedral definitions do not have
to represent real bonded interactions. Following the last atom definition are two optional blank
line separated sets of atom number pairs. The first list contains pairs of atoms that are covalently
bonded, but whose bond length was not used as part of the atom definitions. These pairs are
typically used to close ring structures. The second list contains bonds that are to be broken, i.e.,
pairs of atoms that are not covalently bonded, but which were used to define a distance in the atom
definitions.
SAMPLE.KEY
The keyword parameter file always has the extension .key and is optionally present during Tinker
calculations. It contains values for any of a wide variety of switches and parameters that are used
to change the course of the computation from the default. The detailed contents of this file is
explained in a latter section of this User’s Guide. If a molecular system specific keyfile, in this case
sample.key, is not present, the the Tinker program will look in the same directory for a generic file
named Tinker.key.
SAMPLE.DYN

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The .dyn file contains values needed to restart a molecular or stochastic dynamics computation. It
stores the current position, current velocity and current and previous accelerations for each atom,
as well as the size and shape of any periodic box or crystal unit cell. This information can be used
to start a new dynamics run from the final state of a previous run. Upon startup, the dynamics
programs always check for the presence of a .dyn file and make use of it whenever possible. The
.dyn file is updated concurrent with the saving of a new dynamics trajectory snapshot.
SAMPLE.END
The .end file type provides a mechanism to gracefully stop a running Tinker calculation. At appro-
priate checkpoints during a calculation, Tinker will test for the presence of a sample.end file, and
if found will terminate the calculation after updating the output. The .end file can be created at
any time during a computation, and will be detected when the next checkpoint is reached. The file
may be of zero size, and its contents are unimportant. In the current version of Tinker, the .end
mechanism is only available within dynamics-based programs.
SAMPLE.001, SAMPLE.002, . . . .
Several types of computations produce files containing a three or more digit extension (.001 as
shown; or .002, .137, .5678, etc.). These are referred to as cycle files, and are used to store
various types of output structures. The cycle files from a given computation are identical in internal
structure to either the .xyz or .int files described above. For example, the vibrational analysis
program can save the tenth normal mode in sample.010. A molecular dynamics-based program
might save its tenth 0.1 picosecond frame (or an energy minimizer its tenth partially minimized
intermediate) in a file of the same name.
SAMPLE.LOG
The Force Field Explorer interface to Tinker saves results of all calculations launched from the GUI
to a log file with the .log suffix. Any output that would normally be directed to the screen after
starting a program from the command line is appended to this log file by Force Field Explorer.
SAMPLE.ARC
A Tinker archive file is simply a series of .xyz Cartesian coordinate files appended together one after
another. This file can be used to condense the results from intermediate stages of an optimization,
frames from a molecular dynamics trajectory, or set of normal mode vibrations into a single file for
storage. The Tinker archive file can be displayed as a sequential frame “movie” by the Force Field
Explorer modeling program.
SAMPLE.DCD
The Tinker DCD implementation is a binary trajectory archive file in the CHARMM/XPLOR DCD
format as supported by VMD and other visualization packages. It contains a single header section
with a title, the number of atoms, and other information. This is followed by a section for each
trajectory frame containing the six lattice parameter values and X,Y,Z coordinates. No connectivity
or atom type information is stored. The DCD file can be read by VMD along with a PDB file or
Tinker XYZ file, and then displayed as a sequential frame “movie”.
SAMPLE.PDB
This file type contains coordinate information in the PDB format developed by the Brookhaven
Protein Data Bank for deposition of model structures based on macromolecular X-ray diffraction
and NMR data. Although Tinker itself does not use .pdb files directly for input/output, auxiliary

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programs are provided with the system for interconverting .pdb files with the .xyz format described
above.
SAMPLE.SEQ
This file type contains the primary sequence of a biopolymer in the standard one-letter code with
50 residues per line. The .seq file for a biopolymer is generated automatically when a PDB file
is converted to Tinker .xyz format or when using the PROTEIN or NUCLEIC programs to build
a structure from sequence It is required for the reverse conversion of a Tinker file back to PDB
format..
SAMPLE.FRAC
The fractional coordinates corresponding to the asymmetric unit of a crystal unit cell are stored in
the .frac file. The internal format of this file is identical to the .xyz file; except that the coordinates
are fractional instead of in Angstrom units.
SAMPLE.MOL2
File conversion to and from the Tripos Sybyl MOL2 file format is supported by Tinker. The utility
programs XYZMOL2 and MOL2XYZ transform a Tinker XYZ file to MOL2 format, and the reverse.
SAMPLE.FRC
The .frc file contains the components of the force on the atoms. It consists of a title line followed by
one line for each atom in the structure. Each line contains: the sequential number within the struc-
ture, an atomic symbol or name, X-, Y-, and Z-components of the force in units of kcal/mol/Ang,
the force field atom type number of the atom, and a list of the atoms connected to the current
atom. As controlled by keywords, this file type is optionally written during Tinker optimization or
molecular dynamics calculations.
SAMPLE.UIND
The .uind file contains the components of the induced dipole vector on the atoms. It consists of
a title line followed by one line for each atom in the structure. Each line contains: the sequential
number within the structure, an atomic symbol or name, X-, Y-, and Z-components of the induced
dipole in units of Debye, the force field atom type number of the atom, and a list of the atoms
connected to the current atom. As controlled by keywords, this file type is optionally written
during Tinker optimization or molecular dynamics calculations using polarizable force fields.
PARAMETER FILES (*.PRM)
The potential energy parameter files distributed with the Tinker package all end in the extension
.prm, although this is not required by the programs themselves. Each of these files contains a
definition of the potential energy functional forms for that force field as well as values for indi-
vidual energy parameters. For example, the mm3pro.prm file contains the energy parameters and
definitions needed for a protein-specific version of the MM3 force field.

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12 Chapter 3. Types of Input & Output Files

 CHAPTER

FOUR

POTENTIAL ENERGY PROGRAMS

This section of the manual contains a brief description of each of the Tinker potential energy pro-
grams. A detailed example showing how to run each program is included in a later section. The
programs listed below are all part of the main, supported distribution. Additional source code for
various unsupported programs can be found in the /other directory of the Tinker distribution.
ALCHEMY
ALCHEMY is a simple program to perform very basic free energy perturbation calculations. This
program is provided mostly for demonstration purposes. For example, we use ALCHEMY in a
molecular modeling course laboratory exercise to perform such classic mutations as chloride to
bromide and ethane to methanol in water. The present version uses the perturbation formula
and windowing with an explicit mapping of atoms involved in the mutation (“Amber”-style), in-
stead of thermodynamic integration and independent freely propagating groups of mutated atoms
(“CHARMM”-style). Some of the code specific to this program is limited to the Amber and OPLS po-
tential functional forms, but could be easily generalized to handle other potentials. A more general
and sophisticated version is currently under development.
ANALYZE
ANALYZE provides information about a specific molecular structure. The program will ask for the
name of a structure file, which must be in the Tinker XYZ file format, and the type of analysis
desired. Options allow output of: (1) total potential energy of the system, (2) breakdown of the
energy by potential function type or over individual atoms, (3) computation of the total dipole mo-
ment and its components, moments of inertia and radius of gyration, (4) listing of the parameters
used to compute selected interaction energies, (5) energies associated with specified individual
interactions.
ANNEAL
ANNEAL performs a molecular dynamics simulated annealing computation. The program starts
from a specified input molecular structure in Tinker XYZ format. The trajectory is updated us-
ing either a modified Beeman or a velocity Verlet integration method. The annealing protocol is
implemented by allowing smooth changes between starting and final values of the system tem-
perature via the Groningen method of coupling to an external bath. The scaling can be linear or
sigmoidal in nature. In addition, parameters such as cutoff distance can be transformed along
with the temperature. The user must input the desired number of dynamics steps for both the
equilibration and cooling phases, a time interval for the dynamics steps, and an interval between
coordinate/trajectory saves. All saved coordinate sets along the trajectory are placed in sequentially
numbered cycle files.

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CRITICAL
CRITICAL performs a least squares optimization of the norm of the gradient vector in order to
find the nearest stationary or critical point. It is generally the preferred method for location of
transition states, as long as a reasonable initial starting structure is available. For optimization to
a local minimum structure, CRITICAL will usually converge to loose tolerance more slowly than
MINIMIZE, and to tight tolerance more slowly than NEWTON. Since the program can converge to
any order of stationary point, it is necessary to use the VIBRATE program to identify the number of
negative frequencies at the final structure.
DYNAMIC
DYNAMIC performs a molecular dynamics (MD) or stochastic dynamics (SD) computation. Starts
either from a specified input molecular structure (an XYZ file) or from a structure-velocity-
acceleration set saved from a previous dynamics trajectory (a restart from a DYN file). MD tra-
jectories are propagated using either a modified Beeman or a velocity Verlet integration method.
SD is implemented via our own derivation of a velocity Verlet-based algorithm. In addition the
program can perform full crystal calculations, and can operate in constant energy mode or with
maintenance of a desired temperature and/or pressure using the Berendsen method of coupling
to external baths. The user must input the desired number of dynamics steps, a time interval for
the dynamics steps, and an interval between coordinate/trajectory saves. Coordinate sets along the
trajectory can be saved as sequentially numbered cycle files or directly to a Tinker archive (ARC)
file. At the same time that a point along the trajectory is saved, the complete information needed
to restart the trajectory from that point is updated and stored in the DYN file.
GDA
GDA is a program to implement Straub’s Gaussian Density Annealing algorithm over an effective
series of analytically smoothed potential energy surfaces. This method can be viewed as an ex-
tended stochastic version of the diffusion equation method of Scheraga, et al., and also has many
similar features to the Tinker Potential Smoothing and Search (PSS) series of programs. The cur-
rent version of GDA is similar to but does not exactly reproduce Straub’s published method and
is limited to argon clusters and other simple systems involving only van der Waals interactions;
further modification and development of this code is currently underway in the Ponder research
group. As with other programs involving potential smoothing, GDA currently requires use of the
smooth.prm force field parameters.
MINIMIZE
The MINIMIZE program performs a limited memory L-BFGS minimization of an input structure
over Cartesian coordinates using a modified version of the algorithm of Jorge Nocedal. The method
requires only the potential energy and gradient at each step along the minimization pathway. It
requires storage space proportional to the number of atoms in the structure. The MINIMIZE proce-
dure is recommended for preliminary minimization of trial structures to an RMS gradient of 1.0 to
0.1 kcal/mole/Ang. It has a relatively fast cycle time and is tolerant of poor initial structures, but
converges in a slow, linear fashion near the minimum. The user supplies the name of the Tinker
XYZ coordinates file and a target rms gradient value at which the minimization will terminate.
Output consists of minimization statistics written to the screen or redirected to an output file, and
the new coordinates written to updated XYZ files or to cycle files.
MINIROT

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The MINIROT program uses the same limited memory L-BFGS method as MINIMIZE, but performs
the computation in terms of dihedral angles instead of Cartesian coordinates. Output is saved in
an updated .int file or in cycle files.
MINRIGID
The MINRIGID program is similar to MINIMIZE except that it operates on rigid bodies starting from
a Tinker XYZ coordinate file and the rigid body group definitions found in the corresponding KEY
file. Output is saved in an updated XYZ file or in cycle files.
MONTE
The MONTE program implements the Monte Carlo Minimization algorithm developed by Harold
Scheraga’s group and others. The procedure takes Monte Carlo steps for either a single atom or a
single torsional angle, then performs a minimization before application of the Metropolis sampling
method. This results in effective sampling of a modified potential surface where the only possible
energy levels are those of local minima on the original surface. The program can be easily modified
to elaborate on the available move set.
NEWTON
NEWTON is a truncated Newton minimization method which requires potential energy, gradient
and Hessian information. This procedure has significant advantages over standard Newton meth-
ods, and is able to minimize very large structures completely. Several options are provided with
respect to minimization method and preconditioning of the Newton equations. The default options
are recommended unless the user is familiar with the math involved. This program operates in
Cartesian coordinate space and is fairly tolerant of poor input structures. Typical algorithm itera-
tion times are longer than with nonlinear conjugate gradient or variable metric methods, but many
fewer iterations are required for complete minimization. NEWTON is usually the best choice for
minimizations to the 0.01 to 0.000001 kcal/mole/Ang level of RMS gradient convergence. Tests
for directions of negative curvature can be removed, allowing NEWTON to be used for optimization
to conformational transition state structures (this only works if the starting point is very close to
the transition state). Input consists of a Tinker XYZ coordinates file; output is an updated set of
minimized coordinates and minimization statistics.
NEWTROT
The NEWTROT program is similar to NEWTON except that it requires a .int file as input and then
operates in terms of dihedral angles as the minimization variables. Since the dihedral space Hessian
matrix of an arbitrary structure is often indefinite, this method will often not perform as well as the
other, simpler dihedral angle based minimizers.
OPTIMIZE
The OPTIMIZE program performs a optimally conditioned variable metric minimization of an input
structure over Cartesian coordinates using an algorithm due to William Davidon. The method does
not perform line searches, but requires computation of energies and gradients as well as storage
for an estimate of the inverse Hessian matrix. The program operates on Cartesian coordinates from
a Tinker XYZ file. OPTIMIZE will typically converge somewhat faster and more completely than
MINIMIZE. However, the need to store and manipulate a full inverse Hessian estimate limits its use
to structures containing less than a few hundred atoms on workstation class machines. As with
the other minimizers, OPTIMIZE needs input coordinates and an rms gradient cutoff criterion. The
output coordinates are saved in updated .xyz files or as cycle files.

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OPTIROT
The OPTIROT program is similar to OPTIMIZE except that it operates on dihedral angles starting
from a Tinker INT internal coordinate file. This program is usually the preferred method for most
dihedral angle optimization problems since Truncated Newton methods appear, in our hands, to
lose some of their efficacy in moving from Cartesian to torsional coordinates.
OPTRIGID
The OPTRIGID program is similar to OPTIMIZE except that it operates on rigid bodies starting from
a Tinker XYZ coordinate file and the rigid body atom group definitions found in the corresponding
KEY file. Output is saved in an updated XYZ file or in cycle files.
PATH
The PATH program implements a variant of Elber’s Lagrangian multiplier-based reaction path fol-
lowing algorithm. The program takes as input a pair of structural minima as Tinker XYZ files,
and then generates a user specified number of points along a path through conformational space
connecting the input structures. The intermediate structures are output as Tinker cycle files, and
the higher energy intermediates can be used as input to a Newton-based optimization to locate
conformational transition states.
PSS
PSS implements our version of a potential smoothing and search algorithm for the global optimiza-
tion of molecular conformation. An initial structure in .xyz format is first minimized in Cartesian
coordinates on a series of increasingly smoothed potential energy surfaces. Then the smoothing
procedure is reversed with minimization on each successive surface starting from the coordinates
of the minimum on the previous surface. A local search procedure is used during the backtracking
to explore for alternative minima better than the one found during the current minimization. The
final result is usually a very low energy conformation or, in favorable cases, the global energy min-
imum conformation. The minimum energy coordinate sets found on each surface during both the
forward smoothing and backtracking procedures are placed in sequentially numbered cycle files.
PSSRIGID
PSSRIGID implements the potential smoothing and search method as described above for the PSS
program, but performs the computation in terms of keyfile-defined rigid body atom groups instead
of Cartesian coordinates. Output is saved in numbered cycle files with the XYZ file format.
PSSROT
PSSROT implements the potential smoothing and search method as described above for the PSS
program, but performs the computation in terms of a set of user-specified dihedral angles instead
of Cartesian coordinates. Output is saved in numbered cycle files with the INT file format.
SADDLE
The SADDLE program locates a conformational transition state between two potential energy min-
ima. SADDLE uses a conglomeration of ideas from the Bell-Crighton quadratic path and the
Halgren-Lipscomb synchronous transit methods. The basic idea is to perform a nonlinear con-
jugate gradient optimization in a subspace orthogonal to a suitably defined reaction coordinate.
The program requires as input the coordinates, as Tinker XYZ files, of the two minima and an rms
gradient convergence criterion for the optimization. The current estimate of the transition state

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structure is written to the file TSTATE.XYZ. Crude transition state structures generated by SADDLE
can sometimes be refined using the NEWTON program. Optionally, a scan of the interconversion
pathway can be made at each major iteration.
SCAN
SCAN is a program for general conformational search of an entire potential energy surface via a
basin hopping method. The program takes as input a Tinker XYZ coordinates file which is then min-
imized to find the first local minimum for a search list. A series of activations along various normal
modes from this initial minimum are used as seed points for additional minimizations. Whenever
a previously unknown local minimum is located it is added to the search list. When all minima
on the search list have been subjected to the normal mode activation without locating additional
new minima, the program terminates. The individual local minima are written to cycle files as they
are discovered. While the SCAN program can be used on standard undeformed potential energy
surfaces, we have found it to be most useful for quickly “scanning” a smoothed energy surface to
enumerate the major basins of attraction spaning the entire surface.
SNIFFER
SNIFFER is a program that implements the Sniffer global optimization algorithm of Butler and
Slaminka, a discrete version of Griewank’s global search trajectory method. The program takes
an input Tinker XYZ coordinates file and shakes it vigorously via a modified dynamics trajectory
before, hopefully, settling into a low lying minimum. Some trial and error is often required as the
current implementation is sensitive to various parameters and tolerances that govern the computa-
tion. At present, these parameters are not user accessible, and must be altered in the source code.
However, this method can do a good job of quickly optimizing conformation within a limited range
of convergence.
TESTGRAD
The TESTGRAD program computes and compares the analytical and numerical first derivatives
(i.e., the gradient vector) of the potential energy for a Cartesian coordinate input structure. The
output can be used to test or debug the current potential or any added user defined energy terms.
TESTHESS
The TESTHESS program computes and compares the analytical and numerical second derivatives
(i.e., the Hessian matrix) of the potential energy for a Cartesian coordinate input structure. The
output can be used to test or debug the current potential or any added user defined energy terms.
TESTPAIR
The TESTPAIR program compares the efficiency of different nonbonded neighbor methods for the
current molecular system. The program times the computation of energy and gradient for the
van der Waals and charge-charge electrostatic potential terms using a simple double loop over all
interactions and using the Method of Lights algorithm to select neighbors. The results can be used
to decide whether the Method of Lights has any CPU time advantage for the current structure. Both
methods should give exactly the same answer in all cases, since the identical individual interactions
are computed by both methods. The default double loop method is faster when cutoffs are not used,
or when the cutoff sphere contains about half or more of the total system of unit cell. In cases where
the cutoff sphere is much smaller than the system size, the Method of Lights can be much faster
since it avoids unnecessary calculation of distances beyond the cutoff range.

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TESTPOL
TESTPOL computes and compares several different methods for determining polarization via
atomic induced dipole moments. The available methods include direct polarization (“iAMOEBA”),
mutual SCF iteration to varying levels of convergence (via PCG iteration), perturbation theory ex-
trapolation (OPT2 through OPT6), and truncated conjugate gradient (TCG1 and TCG2) solvers.
The program will also find the best set of OPT coefficients for the system considered.
TESTROT
The TESTROT program computes and compares the analytical and numerical first derivatives (i.e.,
the gradient vector) of the potential energy with respect to dihedral angles. Input is a Tinker INT
internal coordinate file. The output can be used to test or debug the current potential functions or
any added user defined energy terms.
TESTVIR
The TESTVIR program checks the accuracy of the analytical internal virial calculation by compar-
ison against a numerical virial computed from the finite-difference derivative of the energy with
respect to the lattice vectors.
TIMER
TIMER is a simple program to provide timing statistics for energy function calls within the Tinker
package. TIMER requires an input XYZ file and outputs the CPU time (or wall clock time, on some
machine types) needed to perform a specified number of energy, gradient and Hessian evaluations.
TIMEROT
The TIMEROT program is similar to TIMER, only it operates over dihedral angles via input of
a Tinker INT internal coordinate file. In the current version, the torsional Hessian is computed
numerically from the analytical torsional gradient.
VIBBIG
VIBBIG is a specialized program for the computing selected vibrational frequencies of a large input
molecular system using a sliding block iterative method to avoid direct diagonalization of the full
Hessian matrix. As implemented the program will first find the lowest frequency vibration and
proceed to higher frequencies in order.
VIBRATE
VIBRATE is a program to perform vibrational analysis by computing and diagonalizing the full
Hessian matrix (i.e., the second partial derivatives) for an input structure (a Tinker XYZ file).
Eigenvalues and eigenvectors of the mass weighted Hessian (i.e., the vibrational frequencies and
normal modes) are also calculated. Structures corresponding to individual normal mode motions
can be saved in cycle files.
VIBROT
The program VIBROT forms the torsional Hessian matrix via numerical differentiation of the ana-
lytical torsional gradient. The Hessian is then diagonalized and the eigenvalues are output. The
present version does not compute the kinetic energy matrix elements needed to convert the Hes-
sian into the torsional normal modes; this will be added in a later version. The required input is a
Tinker INT internal coordinate file.

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XTALFIT
The XTALFIT program is of use in the automated fitting of potential parameters to crystal structure
and thermodynamic data. XTALFIT takes as input several crystal structures (Tinker XYZ files with
unit cell parameters in corresponding KEY files) as well as information on lattice energies and
dipole moments of monomers. The current version uses a nonlinear least squares optimization to
fit van der Waals and electrostatic parameters to the input data. Bounds can be placed on the values
of the optimization parameters.
XTALMIN
XTALMIN is used to perform full crystal minimizations. The program takes as input the structure
coordinates and unit cell lattice parameters. It then alternates cycles of Newton-style optimiza-
tion of the structure and conjugate gradient optimization of the crystal lattice parameters. This
alternating minimization is slower than more direct optimization of all parameters at once, but
is somewhat more robust in our hands. The symmetry of the original crystal is not enforced, so
interconversion of crystal forms may be observed in some cases.

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20 Chapter 4. Potential Energy Programs

 CHAPTER

FIVE

ANALYSIS & UTILITY PROGRAMS & SCRIPTS

This section of the manual contains a brief description of each of the Tinker structure manipulation,
geometric calculation and auxiliary programs. A detailed example showing how to run each pro-
gram is included in a later section. The programs listed below are all part of the main, supported
distribution. Additional source code for various unsupported programs can be found in the /other
directory of the Tinker distribution.
ARCEDIT
ARCEDIT is a program for concatenating Tinker cycle files into a single archive file; useful for stor-
ing the intermediate results of minimizations, dynamics trajectories, and so on. The program can
also extract individual cycle files from a Tinker XYZ archive or DCD binary archive. Additional
options allow for the folding or unfolding of periodic boundaries across a trajectory, and intercon-
version between the Tinker XYZ and DCD binary formats.
BAR
The BAR program computes a free energy from sampling of adjacent “lambda” windows using the
Bennett acceptance ratio (BAR) algorithm. Input consists of trajectories or configurations sampled
from the adjacent windows, as well as keyfiles and parameters used to define the states for the
simulations. In a first phase, the BAR program computes the energies of all structures from both
simulations under the control of both sets of potential energy parameters, i.e., four sets of numbers
which are written to an intermediate .bar file. In its second phase, BAR reads a .bar file and uses the
free energy perturbation (FEP) and Bennett acceptance ratio formula to compute the free energy,
enthalpy and entropy between the two states.
CORRELATE
The CORRELATE program to compute time correlation functions from collections of Tinker cycle
files. Its use requires a user supplied function property that computes the value of the property
for which a time correlation is desired for two input structures. A sample routine is supplied that
computes either a velocity autocorrelation function or an rms structural superposition as a function
of time. The main body of the program organizes the overall computation in an efficient manner
and outputs the final time correlation function.
CRYSTAL
CRYSTAL is a program for the manipulation of crystal structures including interconversion of frac-
tional and Cartesian coordinates, generation of the unit cell from an asymmetric unit, and building
of a crystalline block of specified size via replication of a single unit cell. The present version

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can handle about 25 of the most common space groups, others can easily be added as needed by
modification of the routine symmetry.
DIFFUSE
DIFFUSE computes the self-diffusion constant for a homogeneous liquid via the Einstein equation.
A previously saved dynamics trajectory is read in and “unfolded” to reverse translation of molecules
due to use of periodic boundary conditions. The average motion over all molecules is then used to
compute the self-diffusion constant. While the current program assumes a homogeneous system,
it should be easy to modify the code to handle diffusion of individual molecules or other desired
effects.
DISTGEOM
The DISTGEOM program performs distance geometry calculations using variations on the classic
metric matrix method. A user specified number of structures consistent with keyfile input distance
and dihedral restraints is generated. Bond length and angle restraints are derived from the input
structure. Trial distances between the triangle smoothed lower and upper bounds can be chosen via
any of several metrization methods, including a very effective partial random pairwise scheme. The
correct radius of gyration of the structure is automatically maintained by choosing trial distances
from Gaussian distributions of appropriate mean and width. The initial embedded structures can be
further refined against a geometric restraint-only potential using either a sequential minimization
protocol or simulated annealing.
DOCUMENT
The DOCUMENT program is provided as a minimal listing and documentation tool. It operates
on the Tinker source code, either individual files or the complete source listing produced by the
command script listing.make, to generate lists of routines, common blocks or valid keywords. In
addition, the program has the ability to output a formatted parameter listing from the standard
Tinker parameter files.
FREEFIX
FREEFIX is a small utility to compute the analytical enthalpy, entropy and free energy associated
with the release of a flat-bottomed harmonic distance restraint between two sites within a simula-
tion system.
INTEDIT
INTEDIT allows interactive inspection and alteration of the internal coordinate definitions and
values of a Tinker structure. If the structure is altered, the user has the option to write out a new
internal coordinates file upon exit.
INTXYZ
The INTXYZ program to convert a Tinker .int internal coordinates formatted file into a Tinker .xyz
Cartesian coordinates formatted file.
MOLXYZ
MOLXYZ is a program for converting a MDL (Molecular Design Limited) MOL file into a Tinker XYZ
Cartesian coordinate file. The current version of the program converts the MDL atoms types into
Tinker “tiny force field” atom types based on atomic number and connectivity (i.e., a tetravalent
carbon is type 64).

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MOL2XYZ
The MOL2XYZ program converts a Tripos Sybyl MOL2 file into a Tinker XYZ Cartesian coordinate
file. The current version of the program converts the Sybyl MOL2 atoms types into Tinker “tiny
force field” atom types based on atomic number and connectivity (i.e., a tetravalent carbon is type
64).
NUCLEIC
The NUCLEIC program automates building of nucleic acid structures. Upon interactive input of
a nucleotide sequence with optional phosphate backbone angles, the program builds internal and
Cartesian coordinates. Standard bond lengths and angles are used. Both DNA and RNA sequences
are supported as are A-, B- and Z-form structures. Double helixes of complementary sequence can
be automatically constructed via a rigid docking of individual strands.
PDBXYZ
PDBXYZ is a program for converting a Brookhaven Protein Data Bank file (a PDB file) into a Tinker
.xyz Cartesian coordinate file. If the PDB file contains only protein/peptide amino acid residues,
then standard protein connectivity is assumed, and transferred to the .xyz file. For non-protein
portions of the PDB file, atom connectivity is determined by the program based on interatomic
distances. The program also has the ability to add or remove hydrogen atoms from a protein as
required by the force field specified during the computation.
POLARIZE
POLARIZE is a simple program for computing molecular polarizability from an atom-based dis-
tributed model of polarizability. POLARIZE implements whichever damped interaction model is
specified via keyfile and parameter settings. A Tinker .xyz file is required as input. The output
consists of the overall polarizability tensor in the global coordinates and its eigenvalues.
POLEDIT
POLEDIT is a program for manipulating and processing polarizable atomic multipole models used
by AMOEBA-like force fields. Its primary purpose is to process distributed multipole analysis (DMA)
or minimum basis iterated stockholder (MBIS) results from output of the GDMA or Multiwfn codes,
respectively. The program defines local coordinate frames, sets atomic polarizabilities, removes
molecular mechanics polarization from the atomic multipoles, averages over symmetrical atoms
and outputs parameters in Tinker format. There are additional invocation options to change lo-
cal coordinate frame definitions or remove intramolecular polarization from an existing multipole
model.
POTENTIAL
The POTENTIAL program performs electrostatic potential comparisons and fitting. POTENTIAL
can compare two different force field electrostatic models via computing the RMS between the
electrostatic potentials on a grid of points outside the molecular envelope. An electrostatic potential
grid can also be generated from quantum chemistry output, and compare against a force field
model. Finally, a flexible fitting of a force field model to an existing potential grid is available.
During potential fitting, restraints can be applied to keep multipole components close to input
values and to enforce specified molecular dipole and quadrupole values. The program can also
take as model input a set of different molecules containing common atom types, as well as multiple
conformations of a single molecule.

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PRMEDIT
PRMEDIT is a program for formatting and renumbering Tinker force field parameter files. When
atom types or classes are added to a parameter file, this utility program has the ability to renumber
all the atom records sequentially, and alter type and class numbers in all other parameter entries to
maintain consistency.
PROTEIN
The PROTEIN program automates building of peptide and protein structures. Upon interactive
input of an amino acid sequence with optional phi/psi/omega/chi angles, D/L chirality, etc., the
program builds internal and Cartesian coordinates. Standard bond lengths and angles are assumed
for the peptide. The program will optionally convert the structure to a cyclic peptide, or add either
or both N- and C-terminal capping groups. Atom type numbers are automatically assigned for the
specified force field. The final coordinates and a sequence file are produced as the output.
RADIAL
The RADIAL program finds the pair radial distribution function between two atom types. The user
supplies the two atom names for which the distribution function is to be computed, and the width
of the distance bins for data analysis. A previously saved dynamics trajectory is read as input. The
raw radial distribution and a spline smoothed version are then output from zero to a distance equal
to half the minimum periodic box dimension. The atom names are matched to the atom name
column of the Tinker .xyz file, independent of atom type.
SPACEFILL
The SPACEFILL program computes the volume and surface areas of molecules. Using a modified
version of Connolly’s original analytical description of the molecular surface, the program deter-
mines either the van der Waals, accessible or molecular (contact/reentrant) volume and surface
area. Both surface area and volume are broken down into their geometric components, and surface
area is decomposed into the convex contribution for each individual atom. The probe radius is
input as a user option, and atomic radii can be set via the keyword file. If Tinker archive files are
used as input, the program will compute the volume and surface area of each structure in the input
file.
SPECTRUM
SPECTRUM is a program to compute a power spectrum from velocity autocorrelation data. As
input, this program requires a velocity autocorrelation function as produced by the CORRELATE
program. This data, along with a user input time step, are Fourier transformed to generate the
spectral intensities over a wavelength range. The result is a power spectrum, and the positions of
the bands are those predicted for an infrared or Raman spectrum. However, the data is not weighted
by molecular dipole moment derivatives as would be required to produce correct IR intensities.
SUPERPOSE
The SUPERPOSE program is used to superimpose two molecular structures in 3-dimensions. A
variety of options for input of the atom sets to be used during the superposition are presented
interactively to the user. The superposition can be mass-weighted if desired, and the coordinates
of the second structure superimposed on the first structure are optionally output. If Tinker archive
files are used as input, the program will compute all pairwise superpositions between structures in
the input files.

24 Chapter 5. Analysis & Utility Programs & Scripts

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TESTSURF
The TESTSURF program computes and compares the accessible surface area, excluded volume and
their first derivatives using various analytical and numerical algorithms for a Cartesian coordinate
input structure. Methods include Richmond’s surface area and gradient, Connolly’s surface area
and volume, Kundrot’s volume gradient, and Koehl’s area, volume and gradients. The output can
be used to test the accuracy and speed of these geometric measures.
TORSFIT
TORSFIT is a program for setting force field parameters for torsional terms by fitting 1-fold to 6-fold
torsional amplitudes to the difference between a quantum chemistry rotational profile and a force
field rotational profile without any torsional terms.
VALENCE
VALENCE is a program for setting force field parameters for local valence terms, either from quan-
tum chemistry data or from embedded empirical rules. [This program is still under development.]
XYZEDIT
XYZEDIT is a program to perform a variety of manipulations on an input Tinker .xyz Cartesian
coordinates formatted file. The present version of the program has the following interactively se-
lectable options: (1) Offset the Numbers of the Current Atoms, (2) Deletion of Individual Specified
Atoms, (3) Deletion of Specified Types of Atoms, (4) Deletion of Atoms outside Cutoff Range, (5)
Insertion of Individual Specified Atoms, (6) Replace Old Atom Type with a New Type, (7) Assign
Connectivities based on Distance, (8) Convert Units from Bohrs to Angstroms, (9) Invert thru Ori-
gin to give Mirror Image, (10) Translate Center of Mass to the Origin, (11) Translate a Specified
Atom to the Origin, (12) Translate and Rotate to Inertial Frame, (13) Move to Specified Rigid Body
Coordinates, (14) Create and Fill a Periodic Boundary Box, (15) Soak Current Molecule in Box
of Solvent, (16) Append another XYZ file to Current One. In most cases, multiply options can be
applied sequentially to an input file. At the end of the editing process, a new version of the original
.xyz file is written as output.
XYZINT
XYZINT converts a Tinker .xyz Cartesian coordinate formatted file into a Tinker .int internal coor-
dinates formatted file. This program can optionally use an existing internal coordinates file as a
template for the connectivity information.
XYZMOL2
XYZMOL2 is a program to convert a Tinker .xyz Cartesian coordinates file into a Tripos Sybyl
MOL2 file. The conversion generates only the MOLECULE, ATOM, BOND and SUBSTRUCTURE
record type in the MOL2 file. Generic Sybyl atom types are used in most cases; while these atom
types may need to be altered in some cases, Sybyl is usually able to correctly display the resulting
MOL2 file.
XYZPDB
The XYZPDB program converts a Tinker .xyz Cartesian coordinate file into a Brookhaven Protein
Data Bank file (a PDB file). A Tinker .seq file with the biopolymer sequence must be present if the
output PDB file is to be formatted as a protein or nucleic acid with a defined sequence.

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26 Chapter 5. Analysis & Utility Programs & Scripts

 CHAPTER

SIX

FORCE FIELD PARAMETER SETS

The Tinker package is distributed with several force field parameter sets, implementing a selection
of widely used literature force fields as well as the Tinker force field currently under construction
in the Ponder lab. We try to exactly reproduce the intent of the original authors of our distributed,
third-party force fields. In all cases the parameter sets have been validated against literature re-
ports, results provided by the original developers, or calculations made with the authentic pro-
grams. With the few exceptions noted below, Tinker calculations can be treated as authentic results
from the genuine force fields. A brief description of each parameter set, including some still in
preparation and not distributed with the current version, is provided below with lead literature
references for the force field:
AMBER94.PRM
Amber ff94 parameters for proteins and nucleic acids. Note that with their “Cornell” force field,
the Kollman group has devised separate, fully independent partial charge values for each of the N-
and C-terminal amino acid residues. At present, the terminal residue charges for Tinker’s version
maintain the correct formal charge, but redistributed somewhat at the alpha carbon atoms from the
original Kollman group values. The total magnitude of the redistribution is less than 0.01 electrons
in most cases.
W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, Jr., D. M. Ferguson, D. C. Spellmeyer,
T. Fox, J. W. Caldwell and P. A. Kollman, A Second Generation Force Field for the Simulation of
Proteins, Nucleic Acids, and Organic Molecules, J. Am. Chem. Soc., 117, 5179-5197 (1995) [ff94]
G. Moyna, H. J. Williams, R. J. Nachman and A. I. Scott, Conformation in Solution and Dynamics
of a Structurally Constrained Linear Insect Kinin Pentapeptide Analogue, Biopolymers, 49, 403-413
(1999) [AIB charges]
W. S. Ross and C. C. Hardin, Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy
Perturbation Studies, J. Am. Chem. Soc., 116, 4363-4366 (1994) [alkali metal ions]
J. Aqvist, Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations, J.
Phys. Chem., 94, 8021-8024, 1990 [alkaline earth Ions, radii adapted for Amber combining rule]
Current force field parameter values and suggested procedures for development of parameters
for additional molecules are available from the Amber web site in the Case lab at Scripps, http:
//amber.scripps.edu/
AMBER96.PRM

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Tinker User's Guide

Amber ff96 parameters for proteins and nucleic acids. The only change from the ff94 parameter
set is in the torsional parameters for the protein phi/psi angles. These values were altered to give
better agreement with changes of ff96 with LMP2 QM results from the Friesner lab on alanine
dipeptide and tetrapeptide.
P. Kollman, R. Dixon, W. Cornell, T. Fox, C. Chipot and A. Pohorille, The Development/ Application
of a ‘Minimalist’ Organic/Biochemical Molecular Mechanic Force Field using a Combination of ab
Initio Calculations and Experimental Data, in Computer Simulation of Biomolecular Systems, W. F.
van Gunsteren, P. K. Weiner, A. J. Wilkinson, eds., Volume 3, 83-96 (1997) [ff96]
Current force field parameter values and suggested procedures for development of parameters
for additional molecules are available from the Amber web site in the Case lab at Scripps, http:
//amber.scripps.edu/
AMBER98.PRM
Amber ff98 parameters for proteins and nucleic acids. The only change from the ff94 parameter
set is in the glycosidic torsional parameters that control sugar pucker.
T. E. Cheatham III, P. Cieplak and P. A. Kollman, A Modified Version of the Cornell et al. Force
Field with Improved Sugar Pucker Phases and Helical Repeat, J. Biomol. Struct. Dyn., 16, 845-862
(1999)
Current force field parameter values and suggested procedures for development of parameters
for additional molecules are available from the Amber web site in the Case lab at Scripps, http:
//amber.scripps.edu/
AMBER99.PRM
Amber ff99 parameters for proteins and nucleic acids. The original partial charges from the ff94
parameter set are retained, but many of the bond, angle and torsional parameters have been revised
to provide better general agreement with experiment.
J. Wang, P. Cieplak and P. A. Kollman, How Well Does a Restrained Electrostatic Potential (RESP)
Model Perform in Calcluating Conformational Energies of Organic and Biological Molecules?, J.
Comput. Chem., 21, 1049-1074 (2000)
Current force field parameter values and suggested procedures for development of parameters
for additional molecules are available from the Amber web site in the Case lab at Scripps, http:
//amber.scripps.edu/
AMBER99SB.PRM
Amber ff99SB parameters for proteins and nucleic acids from the Simmerling lab at Stonybrook
University. Modifies the phi/psi and phi’/psi’ torsional parameters of the ff99 protein force field.
V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg and C. Simmerling, Comparison of Multiple
Amber Force Fields and Development of Improved Protein Backbone Parameters, PROTEINS, 65,
712-725 (2006) [PARM99SB]
AMBER14SB.PRM
Update Amber ff99SB protein parameters with improved backbone and sidechain torsional param-
eters. Also contains the updated OL15 DNA and OL3 RNA parameters values for nucleic acids.

28 Chapter 6. Force Field Parameter Sets

 Tinker User's Guide

J. A. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, K. E. House and C. Simmerling, ff14SB:

Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB, J. Chem.
Theory Comput., 11, 2696-2713 (2015) [Protein ff14SB]
R. Galindo-Murillo, J. C. Robertson, M. Zgarbovic, J. Sponer, M. Otyepka, P. Jureska, T. E.
Cheatham, Assessing the Current State of Amber Force Field Modifications for DNA. J. Chem. The-
ory Comput., 12, 4114–4127 (2016) [DNA OL15]
M. Zgarbova, M. Otyepka, J. Sponer, A. Mladek, P. Banas, T. E. Cheatham, P. Jurecka, Refinement
of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations
of Glycosidic Torsion Profiles, J. Chem. Theory Comput., 7, 2886–2902 (2011) [RNA OL3]
AMBER19SB.PRM
Update Amber ff14SB protein parameters with amino acid-specific backbone CMAP torsion-torsion
coupling values. Also contains the updated OL21 DNA and OL3 RNA parameters values for nucleic
acids. Intended for use with the rigid four-point OPC water model.
C. Tian, K. Kasavajhala, K. Belfon, L. Raguette, H. Huang, A. Migues, J. Bickel, Y. Wang, J. Pincay, Q.
Wu and C. Simmerling. ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against
Quantum Mechanics Energy Surfaces in Solution. J. Chem. Theory Comput., 16, 528–552 (2020)
[Protein ff19SB]
M. Zgarbova, J. Sponer and P. Jurecka, Z-DNA as a Touchstone for Additive Empirical Force Fields
and a Refinement of the Alpha/Gamma DNA Torsions for AMBER, J. Chem. Theory Comput., 17,
6292–6301 (2017) [DNA OL21]
M. Zgarbova, M. Otyepka, J. Sponer, A. Mladek, P. Banas, T. E. Cheatham and P. Jurecka, Re-
finement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical
Calculations of Glycosidic Torsion Profiles, J. Chem. Theory Comput., 7, 2886–2902 (2011) [RNA
OL3]
S. Izadi, R. Anandakrishnan and A. V. Onufriev, Building Water Models: A Different Approach, J.
Phys. Chem. Lett., 5, 3863-3871 (2014) [OPC Water]
A. Sengupta, Z. Li, L. F. Song, P. Li and K. M. Merz Jr., Parameterization of Monovalent Ions for
the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models, J. Chem. Inf. Model., 61, 869-880 (2021)
[Monovalent Ions]
Z. Li, L. F. Song, P. Li and K. M. Merz Jr., systematic Parameterization of Divalent Metal Ions for
the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models, J. Chem. Theory Comput., 16, 4429-4442
(2020) [Divalent Cations]
AMOEBA09.PRM
Parameters for the AMOEBA polarizable atomic multipole force field for a number of small organic
molecules. These values were collected from 2009 and before, with values for each molecule
developed individually via comparison against quantum mechanical and bulk phase data.
P. Ren and J. W. Ponder, A Consistent Treatment of Inter- and Intramolecular Polarization in Molec-
ular Mechanics Calculations, J. Comput. Chem., 23, 1497-1506 (2002)
P. Ren and J. W. Ponder, Polarizable Atomic Multipole Water Model for Molecular Mechanics Sim-
ulation, J. Phys. Chem. B, 107, 5933-5947 (2003)

29
Tinker User's Guide

P. Ren and J. W. Ponder, Ion Solvation Thermodynamics from Simulation with a Polarizable Force
Field, A. Grossfield, J. Am. Chem. Soc., 125, 15671-15682 (2003)
AMOEBABIO09.PRM
A combined biomolecular parameter file with 2009 AMOEBA biopolymer force field, with modi-
fications to the original AMOEBA protein parameters made during 2009, and preliminary nucleic
acid parameters due to Chuanjie Wu
A. Grossfield, P. Ren, J. W. Ponder, Ion Solvation Thermodynamics from Simulation with a Polariz-
able Force Field, J. Am. Chem. Soc., 125, 15671-15682 (2003)
P. Ren and J. W. Ponder, Polarizable Atomic Multipole Water Model for Molecular Mechanics Sim-
ulation, J. Phys. Chem. B, 107, 5933-5947 (2003)
AMOEBABIO18.PRM
An updated AMOEBA biomolecular parameter set based on the published 2013 protein parameters
and 2018 nucleic acid parameters. Ion values taken from work by Zhi Wang, and the revised
Generalized Kirkwood implicit solvent parameterization from Mike Schnieders group.
Y. Shi, Z. Xia, J. Zhang, R. Best, J. W. Ponder and P. Ren, Polarizable Atomic Multipole-Based
AMOEBA Force Field for Proteins, J. Chem. Theory Comput., 9, 4046-4063 (2013)
C. Zhang, C. Lu, Z. Jing, C. Wu, J.-P. Piquemal, J. W. Ponder and P. Ren, AMOEBA Polarizable
Atomic Multipole Force Field for Nucleic Acids, J. Chem. Theory Comput., 14, 2084-2108 (2018)
R. A. Corrigan, G. Qi, A. C. Thiel, J. R. Lynn, B. D. Walker, T. L. Casavant, L. Lagardere, J.-P.
Piquemal, J. W. Ponder, P. Ren and M. J. Schnieders, Implicit Solvents for the Polarizable Atomic
Multipole AMOEBA Force Field, J. Chem. Theory Comput., 17, 2323-2341 (2021)
AMOEBABIO-HFC23.PRM
Modified AMOEBA protein parameters with high field corrections (HFC) from Sameer Varma’s
group at the University of South Florida.
V. Wineman-Fisher, Y. Al-Hamdani, I. Addou, A. Tkatchenko and S. Varma, Ion-Hydroxyl Inter-
actions: From High-Level Quantum Benchmarks to Transferable Polarizable Force Fields, J.
Chem. Theory Comput., 15, 2444-2453 (2019)
V. Wineman-Fisher, J. M. Delgado, P. Nagy, E. Jakobsson, S. A. Pandit and S. Varma, Transferable
Interactions of Li+ and Mg2+ Ions in Polarizable Models, J. Chem. Phys., 153, 104113
(2020)
V. Wineman-Fisher, Y. Al-Hamdani, P. Nagy, A. Tkatchenko and S. Varma, Improved Description
of Ligand Polarization Enhances Transferability of Ion-Ligand Interactions, J. Chem. Phys.,
153, 094115 (2020)
J. M. Delgado, V. Wineman-Fisher, S. A. Pandit and S. Varma, Inclusion of High-Field Target
Data in AMOEBA’s Calibration Improves Predictions of Protein-Ion Interactions, J. Chem.
Inf. Model., 62, 4713-4726 (2022)
J. M. Delgado, P. Nagy and S. Varma, Polarizable AMOEBA Model for Simulating Mg2+-
Protein-Nucleotide Complexes, J. Chem. Inf. Model., 64, 378-392 (2024)
AMOEBAIL22.PRM

30 Chapter 6. Force Field Parameter Sets

 Tinker User's Guide

AMOEBA ionic liquid parameters from Andres Cisneros’ group at the University of Texas at Dallas
as provided in late 2022, and updated in May 2023.
AMOEBAPRO04.PRM
Initial protein parameters for the AMOEBA polarizable atomic multipole force field as determined
in 2004.
J. W. Ponder and D. A. Case, Force Fields for Protein Simulation, Adv. Prot. Chem., 66, 27-85
(2003)
P. Ren and J. W. Ponder, Polarizable Atomic Multipole Water Model for Molecular Mechanics Sim-
ulation, J. Phys. Chem. B, 107, 5933-5947 (2003)
P. Ren, C. Wu and J. W. Ponder, Polarizable Atomic Multipole-Based Molecular Mechanics for Or-
ganic Molecules, J. Chem. Theory Comput., 7, 3143-3161 (2011)
AMOEBAPRO13.prm
Y. Shi, Z. Xia, J. Zhang, R. Best, J. W. Ponder and P. Ren, Polarizable Atomic Multipole-Based
AMOEBA Force Field for Proteins, J. Chem. Theory Comput., 9, 4046-4063 (2013)
P. Ren, C. Wu and J. W. Ponder, Polarizable Atomic Multipole-Based Molecular Mechanics for Or-
ganic Molecules, J. Chem. Theory Comput., 7, 3143-3161 (2011)
J. C. Wu, J.-P. Piquemal, R. Chaudret, P. Reinhardt and P. Ren, Polarizable Molecular Dynamics
Simulation of Zn(II) in Water Using the AMOEBA Force Field, J. Chem. Theory Comput., 6, 2059-
2070 (2010)
A. Grossfield, P. Ren, J. W. Ponder, Ion Solvation Thermodynamics from Simulation with a Polariz-
able Force Field, J. Am. Chem. Soc., 125, 15671-15682 (2003)
P. Ren and J. W. Ponder, Polarizable Atomic Multipole Water Model for Molecular Mechanics Sim-
ulation, J. Phys. Chem. B, 107, 5933-5947 (2003)
CHARMM19.PRM
CHARMM19 united-atom parameters for proteins. The nucleic acid parameter are not yet imple-
mented. There are some differences between authentic CHARMM19 and the Tinker version due
to replacement of CHARMM impropers by torsions for cases that involve atoms not bonded to the
trigonal atom and Tinker’s use of all possible torsions across a bond instead of a single torsion per
bond.
E. Neria, S. Fischer and M. Karplus, Simulation of Activation Free Energies in Molecular Systems,
J. Chem. Phys., 105, 1902-1921 (1996)
L. Nilsson and M. Karplus, Empirical Energy Functions for Energy Minimizations and Dynamics of
Nucleic Acids, J. Comput. Chem., 7, 591-616 (1986)
W. E. Reiher III, Theoretical Studies of Hydrogen Bonding, Ph.D. Thesis, Department of Chemistry,
Harvard University, Cambridge, MA, 1985
CHARMM22.PRM
CHARMM22 all-atom parameters for proteins and lipids. Many of the nucleic acid and small model
compound parameters are not currently implemented.

31
Tinker User's Guide

N. Banavali and A. D. MacKerell, Jr., All-Atom Empirical Force Field for Nucleic Acids: 2) Appli-
cation to Molecular Dynamics Simulations of DNA and RNA in Solution, J. Comput. Chem., 21,
105-120 (2000)
A. D. MacKerrell, Jr., et al., All-Atom Empirical Potential for Molecular Modeling and Dynamics
Studies of Proteins, J. Phys. Chem. B, 102, 3586-3616 (1998) [CHARMM22 Protein]
N. Foloppe and A. D. MacKerell, Jr., All-Atom Empirical Force Field for Nucleic Acids: 1) Parame-
ter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data, J.
Comput. Chem., 21, 86-104 (2000) [CHARMM Nucleic Acid]
A. D. MacKerell, Jr., J. Wiorkeiwicz-Kuczera and M. Karplus, An All-Atom Empirical Energy Function
for the Simulation of Nucleic Acids, J. Am. Chem. Soc., 117, 11946-11975 (1995)
S. E. Feller, D. Yin, R. W. Pastor and A. D. MacKerell, Jr., Molecular Dynamics Simulation of Unsatu-
rated Lipids at Low Hydration: Parametrization and Comparison with Diffraction Studies, Biophys.
J., 73, 2269-2279 (1997) [alkenes]
R. H. Stote and M. Karplus, Zinc Binding in Proteins and Solution - A Simple but Accurate Non-
bonded Representation, Proteins, 23, 12-31 (1995) [zinc ion]
Current parameter values are available from the CHARMM parameter site maintained by Alex
MacKerell at the University of Maryland, Baltimore, http://mackerell.umaryland.edu/CHARMM_
ff_params.html
CHARMM27.PRM
CHARMM27 is a modification of CHARMM22 to include CMAP torsion-torsion coupling parameters
for the protein phi-psi backbone torsions.
A. D. MacKerell, Jr, M. Feig, C. L. Brooks III, “Extending the Treatment of Backbone Energetics
in Protein Force Fields: Limitations of Gas-Phase Quantum Mechanics in Reproducing
Protein Conformational Distributions in Molecular Dynamics Simulations”, J. Comput.
Chem., 25, 1400-1415 (2004) [CMAP Torsion-Torsion Correction]
Current parameter values are available from the CHARMM parameter site maintained by Alex
MacKerell at the University of Maryland, Baltimore, http://mackerell.umaryland.edu/CHARMM_
ff_params.html
CHARMM36.PRM
R. B. Best, X. Zhu, J. Shim, P. E. M. Lopes, J. Mittal, M. Feig and A. D. MacKerell Jr., “Op-
timization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved
Sampling of the Backbone Phi, Psi and Side-Chain Chi1 and Chi2 Dihedral Angles”, J.
Chem. Theory Comput., 8, 3257-3273 (2012) [CHARMM36 Protein]
J. Huang and A. D. MacKerell Jr., “CHARMM36 All-Atom Additive Protein Force Field: Val-
idation Based on Comparison to NMR Data”, J. Comput. Chem., 34, 2135-2145 (2013)
[CHARMM36 Protein Validation]
J. Huang, S. Rauscher, G. Nawrocki, T. Ran, M. Feig, B. L. de Groot, H. Grubmuller and A. D
MacKerell Jr., “CHARMM36m: An Improved Force Field for Folded and Intrinsically Disor-
dered Proteins”, Nature Methods, 14, 71-73 (2017) [CHARMM36m Protein]

32 Chapter 6. Force Field Parameter Sets

 Tinker User's Guide

K. Hart, N. Foloppe, C. M. Baker, E. J. Denning, L. Nilsson and A. D. MacKerell Jr., “Optimization

of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conforma-
tional Equilibrium”, J. Chem. Theory Comput., 8, 348-362 (2012) [CHARMM36 DNA]
E. J. Denning, U. D. Priyakumar, L. Nilsson and A. D. MacKerell Jr., “Impact of 2’-Hydroxyl
Sampling on the Conformational Properties of RNA: Update of the CHARMM All-Atom
Additive Force Field for RNA”, J. Comput. Chem., 32, 1929-1943 (2011) [CHARMM36
RNA]
Current parameter values are available from the CHARMM parameter site maintained by Alex
MacKerell at the University of Maryland, Baltimore, http://mackerell.umaryland.edu/charmm-ff.
shtml
DANG.PRM
L. X. Dang, Development of Nonadditive Intermolecular Potentials Using Molecular Dynam-
ics: Solvation of Li+ and F- Ions in Polarizable Water, J. Chem. Phys., 96, 6970-6977
(1992)
D. E. Smith and L. X. Dang, Interionic Potentials of Mean Force for SrCl2 in Polarizable Water:
A Computer Simulation Study, Chem. Phys. Lett., 230, 209-214 (1994)
L. X. Dang and T.-M. Chang, Molecular Dynamics Study of Water Clusters, Liquid, and Liquid-
Vapor Interface of Water with Many-Body Potentials, J. Chem. Phys., 106, 8149-8159
(1997)
T.-M. Chang and L. X. Dang, Ion Solvation in Polarizable Chloroform: A Molecular Dynamics Study,
J. Phys. Chem. B, 101, 10518-10526 (1997)
T.-M. Chang and L. X. Dang, Detailed Study of Potassium Solvation Using Molecular Dynamics
Techniques, J. Phys. Chem. B, 103, 4714-4720 (1999)
L. X. Dang, Computer Simulation Studies of Ion Transport Across a Liquid/Liquid Interface,
J. Phys. Chem. B, 103, 8195-8200 (1999)
L. X. Dang, Intermolecular Interactions of Liquid Dichloromethane and Equilibrium Properties
of Liquid-Vapor and Liquid-Liquid Interfaces: A Molecular Dynamics Study, J. Chem.
Phys., 110, 10113-10122 (1999)
L. X. Dang and D. Feller, Molecular Dynamics Study of Water-Benzene Interactions at the
Liquid/Vapor Interface of Water, J. Phys. Chem. B, 104, 4403-4407 (2000)
L. X. Dang, Molecular Dynamics Study of Benzene-Benzene and Benzene-Potassium Ion In-
teractions Using Polarizable Potential Models, J. Chem. Phys., 113, 266-273 (2000)
L. X. Dang, Computational Study of Ion Binding to the Liquid Interface of Water, J. Phys.
Chem. B, 106, 10388-10394 (2002)
T.-M. Chang and L. X. Dang, On Rotational Dynamics of an NH4+ in Water, J. Chem. Phys., 118,
8813-8820 (2003)
L. X. Dang, Solvation of the Hydronium Ion at the Water Liquid/Vapor Interface, J. Chem.
Phys., 119, 6351-6353 (2003)
L. X. Dang and T.-M. Chang, Many-Body Interactions in Liquid Methanol and its Liquid/Vapor
Interface: A Molecular Dynamics Study, J. Chem. Phys., 119, 9851-9857 (2003)

33
Tinker User's Guide

L. X. Dang and B. C. Garrett, Molecular Mechanism of Water and Ammonia Uptake by the
Liquid/Vapor Interface of Water, Chem. Phys. Lett., 385, 309-313 (2004)
L. X. Dang, Ions at the Liquid/Vapor Interface of Methanol, J. Phys. Chem. A, 108, 9014-9017
(2004)
M. Roeselova, J. Vieceli, L. X. Dang, B. C. Garrett and D. J. Tobias, Hydroxyl Radical at the
Air-Water Interface, J. Am. Chem. Soc., 126, 16308-16309 (2004)
L. X. Dang, G. K. Schenter, V.-A. Glezakou and J. L. Fulton, Molecular Simulation Analysis and
X-ray Absorption Measurement of Ca2+, K+ and Cl- Ions in Solution, J. Phys. Chem. B,
110, 23644-23654 (2006)
J. L. Thomas, M. Roeselova, L. X. Dang and D. J. Tobias, Molecular Dynamics Simulations of
the Solution-Air Interface of Aqueous Sodium Nitrate, J. Phys. Chem. A, 111, 3091-3098
(2007)
C. D. Wick and L. X. Dang, Molecular Dynamics Study of Ion Transfer and Distribution at the
Interface of Water and 1,2-Dichloroethane, J. Chem. Phys. C, 112, 647-649 (2008)
C. D. Wick and L. X. Dang, “Investigating Hydroxide Anion Interfacial Activity by Classical and
Multistate Empirical Valence Bond Molecular Dynamics Simulations, J. Phys. Chem. A,
113, 6356-6364 (2009)
X. Sun, T.-M. Chang, Y. Cao, S. Niwayama, W. L. Hase and L. X. Dang, Solvation of Dimethyl
Succinate in a Sodium Hydroxide Aqueous Solution. A Computational Study, J. Phys. Chem.
B, 113, 6473-6477 (2009)
M. Baer, C. J. Mundy, T.-M. Chang, F.-M. Tao and L. X. Dang, Interpreting Vibrational Sum-
Frequency Spectra of Sulfur Dioxide at the Air/Water Interface: A Comprehensive Molecular
Dynamics Study, J. Phys. Chem. B, 114, 7245-7249 (2010)
L. X. Dang, T. B. Troung and B. Ginovska-Pangovska, Interionic Potentials of Mean Force for
Ca+2-Cl- in Polarizable Water, J. Chem. Phys., 136, 126101 (2012)
HIPPO19.PRM
Initial parameters for the HIPPO force field for organic molecules, as derived starting in 2019 for
Roseane Silva in the Ponder lab.
J. A. Rackers and J. W. Ponder, Classical Pauli Repulsion: An Anisotropic, Atomic Multipole
Model, J. Chem. Phys., 150, 084104 (2019)
J. A. Rackers, C. Liu, P. Ren and J. W. Ponder, A Physically Grounded Damped Dispersion
Model with Particle Mesh Ewald Summation, J. Chem. Phys., 149, 084115 (2018)
J. A. Rackers, Q. Wang, C. Liu, J.-P. Piquemal, P. Ren and J. W. Ponder, An Optimized Charge
Penetration Model for Use with the AMOEBA Force Field, Phys. Chem. Chem. Phys., 19,
276-291 (2017)
HOCH.PRM
Simple NMR-NOE force field of Hoch and Stern.
J. C. Hoch and A. S. Stern, A Method for Determining Overall Protein Fold from NMR Distance
Restraints, J. Biomol. NMR, 2, 535-543 (1992)

34 Chapter 6. Force Field Parameter Sets

 Tinker User's Guide

IWATER.PRM
Parameters for an AMOEBA-like polarizable multipole model for water including only “direct” (non-
iterative) polarization.
L.-P. Wang, T. L. Head-Gordon, J. W. Ponder, P. Ren, J. D. Chodera, P. K. Eastman, T. J. Martinez
and V. S. Pande, Systematic Improvement of a Classical Model of Water, J. Phys. Chem. B, 117,
9956-9972 (2013)
MM2.PRM
Full MM2(1991) parameters including pi-systems. The anomeric and electronegativity correction
terms included in some later versions of MM2 are not implemented.
N. L. Allinger, Conformational Analysis. 130. MM2. A Hydrocarbon Force Field Utilizing V1 and
V2 Torsional Terms, J. Am. Chem. Soc., 99, 8127-8134 (1977)
J. T. Sprague, J. C. Tai, Y. Yuh and N. L. Allinger, The MMP2 Calculational Method, J. Comput.
Chem., 8, 581-603 (1987)
J. C. Tai and N. L. Allinger, Molecular Mechanics Calculations on Conjugated Nitrogen-Containing
Heterocycles, J. Am. Chem. Soc., 110, 2050-2055 (1988)
J. C. Tai, J.-H. Lii and N. L. Allinger, A Molecular Mechanics (MM2) Study of Furan, Thiophene,
and Related Compounds, J. Comput. Chem., 10, 635-647 (1989)
N. L. Allinger, R. A. Kok and M. R. Imam, Hydrogen Bonding in MM2, J. Comput. Chem., 9, 591-595
(1988)
L. Norskov-Lauritsen and N. L. Allinger, A Molecular Mechanics Treatment of the Anomeric Effect,
J. Comput. Chem., 5, 326-335 (1984)
All parameters distributed with Tinker are from the “MM2 (1991) Parameter Set”, as provided by
N. L. Allinger, University of Georgia
MM3.PRM
Full MM3(2000) parameters including pi-systems. The directional hydrogen bonding term and
electronegativity bond length corrections are implemented, but the anomeric and Bohlmann cor-
rection terms are not implemented.
N. L. Allinger, Y. H. Yuh and J.-H. Lii, Molecular Mechanics. The MM3 Force Field for Hydrocarbons.
1, J. Am. Chem. Soc., 111, 8551-8566 (1989)
J.-H. Lii and N. L. Allinger, Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 2.
Vibrational Frequencies and Thermodynamics, J. Am. Chem. Soc., 111, 8566-8575 (1989)
J.-H. Lii and N. L. Allinger, Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 3. The
van der Waals’ Potentials and Crystal Data for Aliphatic and Aromatic Hydrocarbons, J. Am. Chem.
Soc., 111, 8576-8582 (1989)
N. L. Allinger, H. J. Geise, W. Pyckhout, L. A. Paquette and J. C. Gallucci, Structures of Norbor-
nane and Dodecahedrane by Molecular Mechanics Calculations (MM3), X-ray Crystallography, and
Electron Diffraction, J. Am. Chem. Soc., 111, 1106-1114 (1989) [stretch-torsion cross term]
N. L. Allinger, F. Li and L. Yan, Molecular Mechanics. The MM3 Force Field for Alkenes, J. Comput.
Chem., 11, 848-867 (1990)

35
Tinker User's Guide

N. L. Allinger, F. Li, L. Yan and J. C. Tai, Molecular Mechanics (MM3) Calculations on Conjugated
Hydrocarbons, J. Comput. Chem., 11, 868-895 (1990)
J.-H. Lii and N. L. Allinger, Directional Hydrogen Bonding in the MM3 Force Field. I, J. Phys. Org.
Chem., 7, 591-609 (1994)
J.-H. Lii and N. L. Allinger, Directional Hydrogen Bonding in the MM3 Force Field. II, J. Comput.
Chem., 19, 1001-1016 (1998)
All parameters distributed with Tinker are from the “MM3 (2000) Parameter Set”, as provided by
N. L. Allinger, University of Georgia, August 2000
MM3PRO.PRM
Protein-only version of the MM3 parameters.
J.-H. Lii and N. L. Allinger, The MM3 Force Field for Amides, Polypeptides and Proteins, J. Comput.
Chem., 12, 186-199 (1991)
MMFF94.PRM
Nearly complete implementation of the MMFF94 force field, missing only the parameterization
method for charged heteroaromatic ring systems.
T. A. Halgren, Merck Molecular Force Field. I. Basis, Form, Scope, Parametrization, and Per-
formance of MMFF94, J. Comput. Chem., 17, 490-519 (1995)
T. A. Halgren, Merck Molecular Force Field. II. MMFF94 van der Waals and Electrostatic
Parameters for Intermolecular Interactions, J. Comput. Chem., 17, 520-552 (1995)
T. A. Halgren, Merck Molecular Force Field. III. Molecular Geometries and Vibrational Fre-
quencies for MMFF94, J. Comput. Chem., 17, 553-586 (1995)
T. A. Halgren and R. B. Nachbar, Merck Molecular Force Field. IV. Conformational Energies
and Geometries for MMFF94, J. Comput. Chem., 17, 587-615 (1995)
T. A. Halgren, Merck Molecular Force Field. V. Extension of MMFF94 Using Experimental
Data, Additional Computational Data, and Empirical Rules, J. Comput. Chem., 17, 616-
641 (1995)
T. A. Halgren, MMFF VI. MMFF94s Option for Energy Minimization Studies, J. Comput.
Chem., 20, 720-729 (1999)
T. A. Halgren, MMFF VII. Characterization of MMFF94, MMFF94s, and Other Widely Avail-
able Force Fields for Conformational Energies and for Intermolecular-Interaction Ener-
gies and Geometries, J. Comput. Chem., 20, 730-748 (1999)
MMFF94S.PRM
The MMFF94s parameter set enforces greater planarity at certain trigonal nitrogen atoms, including
amides, anilines, ureas and others. It is meant to mimic the average bulk phase structure at these
nitrogen centers. The changes from MMFF94 are only in out-of-plane and torsional parameters.
T. A. Halgren, MMFF VI. MMFF94s Option for Energy Minimization Studies, J. Comput.
Chem., 20, 720-729 (1999)

36 Chapter 6. Force Field Parameter Sets

 Tinker User's Guide

OPLSUA.PRM
Complete OPLS-UA with united-atom parameters for proteins and many classes of organic
molecules. Explicit hydrogens on polar atoms and aromatic carbons.
W. L. Jorgensen and J. Tirado-Rives, The OPLS Potential Functions for Proteins. Energy Minimiza-
tions for Crystals of Cyclic Peptides and Crambin, J. Am. Chem. Soc., 110, 1657-1666 (1988)
[peptide and proteins]
W. L. Jorgensen and D. L. Severance, Aromatic-Aromatic Interactions: Free Energy Profiles for the
Benzene Dimer in Water, Chloroform, and Liquid Benzene, J. Am. Chem. Soc., 112, 4768-4774
(1990) [aromatic hydrogens]
S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, Jr. and P.
Weiner, A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins, J.
Am. Chem. Soc., 106, 765-784 (1984) [united-atom “AMBER/OPLS” local geometry]
S. J. Weiner, P. A. Kollman, D. T. Nguyen and D. A. Case, An All Atom Force Field for Simulations of
Proteins and Nucleic Acids, J. Comput. Chem., 7, 230-252 (1986) [all-atom “AMBER/OPLS” local
geometry]
L. X. Dang and B. M. Pettitt, Simple Intramolecular Model Potentials for Water, J. Phys. Chem., 91,
3349-3354 (1987) [flexible TIP3P and SPC water]
W. L. Jorgensen, J. D. Madura and C. J. Swenson, Optimized Intermolecular Potential Functions for
Liquid Hydrocarbons, J. Am. Chem. Soc., 106, 6638-6646 (1984) [hydrocarbons]
W. L. Jorgensen, E. R. Laird, T. B. Nguyen and J. Tirado-Rives, Monte Carlo Simulations of Pure
Liquid Substituted Benzenes with OPLS Potential Functions, J. Comput. Chem., 14, 206-215 (1993)
[substituted benzenes]
E. M. Duffy, P. J. Kowalczyk and W. L. Jorgensen, Do Denaturants Interact with Aromatic Hydro-
carbons in Water?, J. Am. Chem. Soc., 115, 9271-9275 (1993) [benzene, naphthalene, urea,
guanidinium, tetramethyl ammonium]
W. L. Jorgensen and C. J. Swenson, Optimized Intermolecular Potential Functions for Amides and
Peptides. Structure and Properties of Liquid Amides, J. Am. Chem. Soc., 106, 765-784 (1984)
[amides]
W. L. Jorgensen, J. M. Briggs and M. L. Contreras, Relative Partition Coefficients for Organic Solutes
form Fluid Simulations, J. Phys. Chem., 94, 1683-1686 (1990) [chloroform, pyridine, pyrazine,
pyrimidine]
J. M. Briggs, T. B. Nguyen and W. L. Jorgensen, Monte Carlo Simulations of Liquid Acetic Acid and
Methyl Acetate with the OPLS Potential Functions, J. Phys. Chem., 95, 3315-3322 (1991) [acetic
acid, methyl acetate]
H. Liu, F. Muller-Plathe and W. F. van Gunsteren, A Force Field for Liquid Dimethyl Sulfoxide and
Physical Properties of Liquid Dimethyl Sulfoxide Calculated Using Molecular Dynamics Simulation,
J. Am. Chem. Soc., 117, 4363-4366 (1995) [dimethyl sulfoxide]
J. Gao, X. Xia and T. F. George, Importance of Bimolecular Interactions in Developing Empirical
Potential Functions for Liquid Ammonia, J. Phys. Chem., 97, 9241-9246 (1993) [ammonia]

37
Tinker User's Guide

J. Aqvist, Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations, J.
Phys. Chem., 94, 8021-8024 (1990) [metal ions]
W. S. Ross and C. C. Hardin, Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy
Perturbation Studies, J. Am. Chem. Soc., 116, 4363-4366 (1994) [alkali metal ions]
J. Chandrasekhar, D. C. Spellmeyer and W. L. Jorgensen, Energy Component Analysis for Dilute
Aqueous Solutions of Li+, Na+, F-, and Cl- Ions, J. Am. Chem. Soc., 106, 903-910 (1984) [halide
ions]
Most parameters distributed with Tinker are from “OPLS and OPLS-AA Parameters for Organic
Molecules, Ions, and Nucleic Acids” as provided by W. L. Jorgensen, Yale University, October 1997
OPLSAA08.PRM
OPLS-UA and OPLS-AA force fields with parameters for proteins and many general classes of or-
ganic molecules.
W. L. Jorgensen, D. S. Maxwell and J. Tirado-Rives, Development and Testing of the OPLS All-Atom
Force Field on Conformational Energetics and Properties of Organic Liquids, J. Am. Chem. Soc.,
117, 11225-11236 (1996)
D. S. Maxwell, J. Tirado-Rives and W. L. Jorgensen, A Comprehensive Study of the Rotational
Energy Profiles of Organic Systems by Ab Initio MO Theory, Forming a Basis for Peptide Torsional
Parameters, J. Comput. Chem., 16, 984-1010 (1995)
W. L. Jorgensen and N. A. McDonald, Development of an All-Atom Force Field for Heterocycles.
Properties of Liquid Pyridine and Diazenes, THEOCHEM-J. Mol. Struct., 424, 145-155 (1998)
N. A. McDonald and W. L. Jorgensen, Development of an All-Atom Force Field for Heterocycles.
Properties of Liquid Pyrrole, Furan, Diazoles, and Oxazoles, J. Phys. Chem. B, 102, 8049-8059
(1998)
R. C. Rizzo and W. L. Jorgensen, OPLS All-Atom Model for Amines: Resolution of the Amine Hy-
dration Problem, J. Am. Chem. Soc., 121, 4827-4836 (1999)
M. L. P. Price, D. Ostrovsky and W. L. Jorgensen, Gas-Phase and Liquid-State Properties of Esters,
Nitriles, and Nitro Compounds with the OPLS-AA Force Field, J. Comput. Chem., 22, 1340-1352
(2001)
The parameters distributed with Tinker are from “OPLS All-Atom Parameters for Organic Molecules,
Ions, Peptides & Nucleic Acids, July 2008” as provided by W. L. Jorgensen, Yale University during
June 2009
OPLSAAL.PRM
An improved OPLS-AA parameter set for proteins in which the only change is a reworking of many
of the backbone and sidechain torsional parameters to give better agreement with LMP2 QM cal-
culations. This parameter set is also known as OPLS(2000).
G. A. Kaminsky, R. A. Friesner, J. Tirado-Rives and W. L. Jorgensen, Evaluation and Reparametriza-
tion of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical
Calculations on Peptides, J. Phys. Chem. B, 105, 6474-6487 (2001)
SMOOTH.PRM

38 Chapter 6. Force Field Parameter Sets

 Tinker User's Guide

Version of OPLS-UA for use with potential smoothing. Largely adapted largely from standard OPLS-
UA parameters with modifications to the vdw and improper torsion terms.
R. V. Pappu, R. K. Hart and J. W. Ponder, Analysis and Application of Potential Energy Smoothing
and Search Methods for Global Optimization, J. Phys, Chem. B, 102, 9725-9742 (1998) [smoothing
modifications]
SMOOTHAA.PRM
Version of OPLS-AA for use with potential smoothing. Largely adapted largely from standard OPLS-
AA parameters with modifications to the vdw and improper torsion terms.
R. V. Pappu, R. K. Hart and J. W. Ponder, Analysis and Application of Potential Energy Smoothing
and Search Methods for Global Optimization, J. Phys, Chem. B, 102, 9725-9742 (1998) [smoothing
modifications]
UWATER.PRM
An AMOEBA-like water model with only a single polarizable site centered on the water oxygen
atom.
R. Qi, L.-P. Wang, Q. Wang, V. S. Pande, P. Ren, “United Polarizable Multipole Water Model for
Molecular Mechanics Simulations”, J. Chem. Phys., 143, 014504 (2015)
WATER03.PRM
The AMOEBA water parameters for a polarizable atomic multipole electrostatics model. This model
from 2003 gives good agreement with ab initio and experimental data for many bulk and cluster
properties.
P. Ren and J. W. Ponder, A Polarizable Atomic Multipole Water Model for Molecular Mechanics
Simulation, J. Phys. Chem. B, 107, 5933-5947 (2003)
P. Ren and J. W. Ponder, Ion Solvation Thermodynamics from Simulation with a Polarizable Force
Field, A. Grossfield, J. Am. Chem. Soc., 125, 15671-15682 (2003)
P. Ren and J. W. Ponder, Temperature and Pressure Dependence of the AMOEBA Water Model, J.
Phys. Chem. B, 108, 13427-13437 (2004)
An earlier version the AMOEBA water model is described in: Yong Kong, Multipole Electrostatic
Methods for Protein Modeling with Reaction Field Treatment, Biochemistry & Molecular Biophysics,
Washington University, St. Louis, August, 1997 [available from http://dasher.wustl.edu/ponder/]
WATER14.PRM
Revision of the AMOEBA 2003 water model based on fitting to high-level QM data on clusters via
use of the Force Balance method of Leeping Wang at the University of California, Davis.
M. L. Laury, L.-P. Wang, V. S. Pande, T. Head-Gordon and J. W. Ponder, Revised Parameters
for the AMOEBA Polarizable Atomic Multipole Water Model, J. Phys. Chem. B., 119,
9423-9437 (2015)
WATER21.PRM
Water parameters for the HIPPO (Hydrogen-like Intermolecular Polarizable Potential) force field. It
accounts for charge penetration, damped dispersion, and anisotropic repulsion as per the published
HIPPO theory papers.

39
Tinker User's Guide

J. A. Rackers, R. R. Silva and J. W. Ponder, A Polarizable Water Model Derived from a Model
Electron Density, J. Chem. Theory Comput., 17, 7056-7084 (2021)
J. A. Rackers and J. W. Ponder, Classical Pauli Repulsion: An Anisotropic, Atomic Multipole Model,
J. Chem. Phys., 150, 084104 (2019)
J. A. Rackers, C. Liu, P. Ren and J. W. Ponder, A Physically Grounded Damped Dispersion Model
with Particle Mesh Ewald Summation, J. Chem. Phys., 149, 084115 (2018)
J. A. Rackers, Q. Wang, C. Liu, J.-P. Piquemal, P. Ren and J. W. Ponder, An Optimized Charge
Penetration Model for Use with the AMOEBA Force Field, Phys. Chem. Chem. Phys., 19, 276-291
(2017)
WATER22.PRM
An improved AMOEBA water model derived by Chengwen Liu at Univ. of Texas at Austin. Tun-
able parameters are vdw and bond/angle constants, the model provides excellent agreement with
experiment and high-quality QM data

40 Chapter 6. Force Field Parameter Sets

 CHAPTER

SEVEN

SPECIAL FEATURES & METHODS

This section contains several short notes with further information about Tinker methodology, algo-
rithms and special features. The discussion is not intended to be exhaustive, but rather to explain
features and capabilities so that users can make more complete use of the package.

7.1 File Version Numbers

All of the input and output file types routinely used by the Tinker package are capable of existing as
multiple versions of a base file name. For example, if the program XYZINT is run on the input file
molecule.xyz, the output internal coordinates file will be written to molecule.int. If a file named
molecule.int is already present prior to running XYZINT, then the output will be written instead
to the next available version, in this case to molecule.int_2. In fact the output is generally written
to the lowest available, previously unused version number (molecule.int_3, molecule.int_4, etc.,
as high as needed). Input file names are handled similarly. If simply molecule or molecule.xyz is
entered as the input file name upon running XYZINT, then the highest version of molecule.xyz will
be used as the actual input file. If an explicit version number is entered as part of the input file
name, then the specified version will be used as the input file.
The version number scheme will be recognized by many older users as a holdover from the VMS
origins of the first version of the Tinker software. It has been maintained to make it easier to chain
together multiple calculations that may create several new versions of a given file, and to make it
more difficult to accidently overwrite a needed result. The version scheme applies to most uses of
many common Tinker file types such as .xyz, .int, .key, .arc. It is not used when an overwritten
file update is obviously the correct action, for example, the .dyn molecular dynamics restart files.
For those users who prefer a more Unix-like operation, and do not desire use of file versions, this
feature can be turned off by adding the NOVERSION keyword to the applicable Tinker keyfile.
The version scheme as implemented in Tinker does have two known quirks. First, it becomes
impossible to directly use the original unversioned copy of a file if higher version numbers are
present. For example, if the files molecule.xyz and molecule.xyz_2 both exist, then molecule.xyz
cannot be accessed as input by XYZINT. If molecule.xyz is entered in response to the input file
name question, molecule.xyz_2 (or the highest present version number) will be used as input.
The only workaround is to copy or rename molecule.xyz to something else, say molecule.new, and
use that name for the input file. Secondly, missing version numbers always end the search for
the highest available version number; i.e., version numbers are assumed to be consecutive and
without gaps. For example, if molecule.xyz, molecule.xyz_2 and molecule.xyz_4 are present, but

41
Tinker User's Guide

not molecule.xyz_3, then molecule.xyz_2 will be used as input to XYZINT if molecule is given as
the input file name. Similarly, output files will fill in gaps in an already existing set of file versions.

7.2 Command Line Options

Most of the Tinker programs support a selection of command line arguments and options. Many
programs will take all the usual interactive input on the original command line used to invoke the
program.
The name of the keyfile to be used for a calculation is read from the argument following a -k
(equivalent to either -key or -keyfile, case insensitive) command line argument. Note that the -k
options can appear anywhere on the command line following the executable name.
Similar to the keyfile option just described, the number of OpenMP threads to be used during a
calculation can be specified as -t (equivalent to -threads, case insensitive) followed by an integer
number.
All other command line arguments, excepting the name of the executable program itself, are treated
as input arguments. These input arguments are read from left to right and interpreted in order as
the answers to questions that would be asked by an interactive invocation of the same Tinker
program. For example, the following command line:
newton molecule -k test a a 0.01
will invoke the NEWTON program on the structure file molecule.xyz using the keyfile test.key,
automatic mode [a] for both the method and preconditioning, and 0.01 for the RMS gradient per
atom termination criterion in kcal/mole/Ang. Provided that the force field parameter set, etc. is
provided in test.key, the above compuation will procede directly from the command line invocation
without further interactive input.

7.3 Use on Windows Systems

Tinker executables for Microsoft PC systems should be run from the DOS or Command Prompt
window available under the various versions of Windows. The Tinker executable directory should
be added to your path via the autoexec.bat file or similar. If a Command Prompt window, set the
number of scrollable lines to a very large number, so that you will be able to inspect screen output
after it moves by. Alternatively, Tinker programs which generate large amounts of screen output
should be run such that output will be redirected to a file. This can be accomplished by running the
Tinker program in batch mode or by using the build-in Unix-like output redirection. For example,
the command:
dynamic < molecule.inp > molecule.log
will run the Tinker dynamic program taking input from the file molecule.inp and sending output
to molecule.log. Also note that command line options as described above are available with the
distributed Tinker executables.
If the distributed Tinker executables are run directly from Windows by double clicking on the
program icon, then the program will run in its own window. However, upon completion of the

42 Chapter 7. Special Features & Methods

 Tinker User's Guide

program the window will close and screen output will be lost. Any output files written by the
program will, of course, still be available. The Windows behavior can be changed by adding the
EXIT-PAUSE keyword to the keyfile. This keyword causes the executation window to remain open
after completion until the “Return/Enter” key is pressed.
An alternative to Command Prompt windows is to use the PowerShell window available on Win-
dows 10 systems, which provides a better emulation of many of the standard features of Linux
shells and MacOS Terminal.
Yet another alternative, particularly attractive to those already familiar with Linux or Unix systems,
is to download the Cygwin package currently available under GPL license from the site http://
source.redhat.com/cygwin/. The cygwin tools provide many of the GNU tools, including a bash
shell window from which Tinker programs can be run.
Finally on Windows 10 systems, it is possible to download and install the Windows Subsystem for
Linux (WSL), and then run the Tinker Linux executables from within WSL.

7.4 Use on MacOS Systems

The command line versions of the Tinker executables are best run on MacOS in a “Terminal” appli-
cation window where behavior is essentially identical to that in a Linux terminal.

7.5 Atom Types vs. Atom Classes

Manipulation of atom types and the proliferation of parameters as atoms are further subdivided into
new types is the bane of force field calculation. For example, if each topologically distinct atom
arising from the 20 natural amino acids is given a different atom type, then about 300 separate
type are required (this ignores the different N- and C-terminal forms of the residues, diastereotopic
hydrogens, etc.). However, all these types lead to literally thousands of different force field pa-
rameters. In fact, there are many thousands of distinct torsional parameters alone. It is impossible
at present to fully optimize each of these parameters; and even if we could, a great many of the
parameters would be nearly identical. Two somewhat complimentary solutions are available to
handle the proliferation of parameters. The first is to specify the molecular fragments to which
a given parameter can be applied in terms of a chemical structure language, SMILES strings for
example.
A second general approach is to use hierarchical cascades of parameter groups. Tinker uses a
simple version of this scheme. Each Tinker force field atom has both an atom type number and
an atom class number. The types are subsets of the atom classes, i.e., several different atom types
can belong to the same atom class. Force field parameters that are somewhat less sensitive to local
environment, such as local geometry terms, are then provided and assigned based on atom class.
Other energy parameters, such as electrostatic parameters, that are very environment dependent
are assigned over the atom types. This greatly reduces the number of independent multiple-atom
parameters like the four-atom torsional parameters.

7.4. Use on MacOS Systems 43

Tinker User's Guide

7.6 Calculations on Partial Structures

Two methods are available for performing energetic calculations on portions or substructures within
a full molecular system. Tinker allows division of the entire system into active and inactive parts
which can be defined via keywords. In subsequent calculations, such as minimization or dynamics,
only the active portions of the system are allowed to move. The force field engine responds to
the active/inactive division by computing all energetic interactions involving at least one active
atom; i.e., any interaction whose energy can change with the motion of one or more active atoms
is computed.
The second method for partial structure computation involves dividing the original system into a
set of atom groups. As before, the groups can be specified via appropriate keywords. The current
Tinker implementation allows specification of up to a maximum number of groups as given in the
sizes.i dimensioning file. The groups must be disjoint in that no atom can belong to more than one
group. Further keywords allow the user to specify which intra- and intergroup sets of energetic
interactions will contribute to the total force field energy. Weights for each set of interactions in
the total energy can also be input. A specific energetic interaction is assigned to a particular intra-
or intergroup set if all the atoms involved in the interaction belong to the group (intra-) or pair of
groups (inter-). Interactions involving atoms from more than two groups are not computed.
Note that the groups method and active/inactive method use different assignment procedures for
individual interactions. The active/inactive scheme is intended for situations where only a portion
of a system is allowed to move, but the total energy needs to reflect the presence of the remaining
inactive portion of the structure. The groups method is intended for use in rigid body calculations,
and is needed for certain kinds of free energy perturbation calculations.

7.7 Metal Complexes and Hypervalent Species

The distribution version of Tinker comes dimensioned for a maximum atomic coordination number
of four as needed for standard organic compounds. In order to use Tinker for calculations on species
containing higher coordination numbers, simply change the value of the parameter maxval in the
master dimensioning file sizes.i and rebuilt the package. Note that this parameter value should not
be set larger than necessary since large values can slow the execution of portions of some Tinker
programs.
Many molecular mechanics approaches to inorganic and metal structures use an angle bending
term which is softer than the usual harmonic bending potential. Tinker implements a Fourier
bending term similar to that used by the Landis group’s SHAPES force field. The parameters for
specific Fourier angle terms are supplied via the ANGLEF parameter and keyword format. Note that
a Fourier term will only be used for a particular angle if a corresponding harmonic angle term is
not present in the parameter file.
We previously worked with the Anders Carlsson group at Washington University in St. Louis to add
their transition metal ligand field term to Tinker. Support for this additional potential functional
form is present in the distributed Tinker source code. We plan to develop energy routines and
parameterization around alternative forms for handling transition metals, including the ligand field
formulation proposed by Rob Deeth and coworkers.

44 Chapter 7. Special Features & Methods

 Tinker User's Guide

7.8 Neighbor Methods for Nonbonded Terms

In addition to standard double loop methods, the Method of Lights is available to speed neighbor
searching. This method based on taking intersections of sorted atom lists can be much faster for
problems where the cutoff distance is significantly smaller than half the maximal cell dimension.
The current version of Tinker does not implement the “neighbor list” schemes common to many
other simulation packages.

7.9 Periodic Boundary Conditions

Both spherical cutoff images or replicates of a cell are supported by all Tinker programs that im-
plement periodic boundary conditions. Whenever the cutoff distance is too large for the minimum
image to be the only relevant neighbor (i.e., half the minimum box dimension for orthogonal cells),
Tinker will automatically switch from the image formalism to use of replicated cells.

7.10 Distance Cutoffs for Energy Functions

Polynomial energy switching over a window is used for terms whose energy is small near the cutoff
distance. For monopole electrostatic interactions, which are quite large in typical cutoff ranges,
a two polynomial multiplicative-additive shifted energy switch unique to Tinker is applied. The
Tinker method is similar in spirit to the force switching methods of Steinbach and Brooks, J. Com-
put. Chem., 15, 667-683 (1994). While the particle mesh Ewald method is preferred when periodic
boundary conditions are present, Tinker’s shifted energy switch with reasonable switching windows
is quite satisfactory for most routine modeling problems. The shifted energy switch minimizes the
perturbation of the energy and the gradient at the cutoff to acceptable levels. Problems should
arise only if the property you wish to monitor is known to require explicit inclusion of long range
components (i.e., calculation of the dielectric constant, etc.).

7.11 Ewald Summations Methods

Tinker contains a versions of the Ewald summation technique for inclusion of long range electro-
static interactions via periodic boundaries. The particle mesh Ewald (PME) method is available
for simple charge-charge potentials, while regular Ewald is provided for polarizable atomic mul-
tipole interactions. The accuracy and speed of the regular and PME calculations is dependent on
several interrelated parameters. For both methods, the Ewald coefficient and real-space cutoff dis-
tance must be set to reasonable and complementary values. Additional control variables for regular
Ewald are the fractional coverage and number of vectors used in reciprocal space. For PME the ad-
ditional control values are the B-spline order and charge grid dimensions. Complete control over
all of these parameters is available via the Tinker keyfile mechanism. By default Tinker will select a
set of parameters which provide a reasonable compromise between accuracy and speed, but these
should be checked and modified as necessary for each individual system.

7.8. Neighbor Methods for Nonbonded Terms 45

Tinker User's Guide

7.12 Continuum Solvation Models

Several alternative continuum solvation algorithms are contained within Tinker. All of these are
accessed via the SOLVATE keyword and its modifiers. Two simple surface area methods are im-
plemented: the ASP method of Eisenberg and McLachlan, and the SASA method from Scheraga’s
group. These methods are applicable to any of the standard Tinker force fields. Various schemes
based on the generalized Born formalism are also available: the original 1990 numerical “Onion-
shell” GB/SA method from Still’s group, the 1997 analytical GB/SA method also due to Still, a
pairwise descreening algorithm originally proposed by Hawkins, Cramer and Truhlar, and the an-
alytical continuum solvation (ACE) method of Schaefer and Karplus. At present, the generalized
Born methods should only be used with force fields having simple partial charge electrostatic inter-
actions.
Some further comments are in order regarding the GB/SA-style solvation models. The Onion-
shell model is provided mostly for comparison purposes. It uses an exact, analytical surface area
calculation for the cavity term and the numerical scheme described in the original paper for the
polarization term. This method is very slow, especially for large systems, and does not contain the
contribution of the Born radii chain rule term to the first derivatives. We recommend its use only
for single-point energy calculations. The other GB/SA methods (“analytical” Still, H-C-T pairwise
descreening, and ACE) use an approximate cavity term based on Born radii, and do contain fully
correct derivatives including the Born radii chain rule contribution. These methods all scale in
CPU time with the square of the size of the system, and can be used with minimization, molecular
dynamics and large molecules.
Finally, we note that the ACE solvation model should not be used with the current version of Tinker.
The algorithm is fully implemented in the source code, but parameterization is not complete. As
of late 2000, parameter values are only available in the literature for use of ACE with the older
CHARMM19 force field. We plan to develop values for use with more modern all-atom force fields,
and these will be incorporated into Tinker sometime in the future.

7.13 Polarizable Multipole Electrostatics

Atomic multipole electrostatics through the quadrupole moment is supported by the current ver-
sion of Tinker, as is either mutual or direct dipole polarization. Ewald summation is available for
inclusion of long range interactions. Calculations are implemented via a mixture of the CCP5 algo-
rithms of W. Smith and the Applequist-Dykstra Cartesian polytensor method. At present analytical
energy and Cartesian gradient code is provided.
The Tinker package allows intramolecular polarization to be treated via a version of the interaction
damping scheme of Thole. To implement the Thole scheme, it is necessary to set all the mutual-
1x-scale keywords to a value of one. The other polarization scaling keyword series, direct-1x-scale
and polar-1x-scale, can be set independently to enable a wide variety of polarization models. In
order to use an Applequist-style model without polarization damping, simply set the polar-damp
keyword to zero.

46 Chapter 7. Special Features & Methods

 Tinker User's Guide

7.14 Potential Energy Smoothing

Versions of our Potential Smoothing and Search (PSS) methodology have been implemented within
Tinker. This methods belong to the same general family as Scheraga’s Diffusion Equation Method,
Straub’s Gaussian Density Annealing, Shalloway’s Packet Annealing and Verschelde’s Effective Dif-
fused Potential, but our algorithms reflect our own ongoing research in this area. In many ways the
Tinker potential smoothing methods are the deterministic analog of stochastic simulated annealing.
The PSS algorithms are very powerful, but are relatively new and are still undergoing modification,
testing and calibration within our research group. This version of Tinker also includes a basin-
hopping conformational scanning algorithm in the program SCAN which is particularly effective on
smoothed potential surfaces.

7.15 Distance Geometry Metrization

A much improved and very fast random pairwise metrization scheme is available which allows
good sampling during trial distance matrix generation without the usual structural anomalies and
CPU constraints of other metrization procedures. An outline of the methodology and its appli-
cation to NMR NOE-based structure refinement is described in the paper by Hodsdon, et al. in
Journal of Molecular Biology, 264, 585-602 (1996). We have obtained good results with something
like the keyword phrase trial-distribution pairwise 5, which performs 5% partial random pairwise
metrization. For structures over several hundred atoms, a value less than 5 for the percentage of
metrization should be fine.

7.14. Potential Energy Smoothing 47

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48 Chapter 7. Special Features & Methods

 CHAPTER

EIGHT

USE OF THE KEYWORD CONTROL FILE

8.1 Using Keywords to Control Tinker Calculations

This section contains detailed descriptions of the keyword parameters used to define or alter the
course of a Tinker calculation. The keyword control file is optional in the sense that all of the
Tinker programs will run in the absence of a keyfile and will simply use default values or query the
user for needed information. However, the keywords allow use of a wide variety of algorithmic and
procedural options, many of which are unavailable interactively.
Keywords are read from the keyword control file. All programs look first for a keyfile with the same
base name as the input molecular system and ending in the extension .key. If this file does not exist,
then Tinker tries to use a generic keyfile with the name tinker.key and located in the same directory
as the input molecular system. The name of the keyfile can also be specified on the command line
invoking a Tinker calculation with the “-k” flag. For example, the command:
analyze my-molecule -k my-keyfile
will run the Tinker ANALYZE program taking as input the molecular system given in the file “my-
molecule” or “my-molecule.xyz”, and using a keyfile named either “my-keyfile” or “my-keyfile.key”.
If a keyfile is not located via any of the above mechanisms, Tinker will continue by using default
values for keyword options and asking interactive questions as necessary.
Tinker searches the keyfile during the course of a calculation for relevant keywords that may be
present. All keywords must appear as the first word on the line. Any blank space to the left of
the keyword is ignored, and all contents of the keyfiles are case insensitive. Some keywords take
modifiers; i.e., Tinker looks further on the same line for additional information, such as the value
of some parameter related to the keyword. Modifier information is read in free format, but must be
completely contained on the same line as the original keyword. Any lines contained in the keyfile
which do not qualify as valid keyword lines are treated as comments and are ignored.
Several keywords take a list of integer values (atom numbers, for example) as modifiers. For these
keywords the integers can simply be listed explicitly and separated by spaces, commas or tabs. If
a range of numbers is desired, it can be specified by listing the negative of the first number of the
range, followed by a separator and the last number of the range. For example, the keyword line
ACTIVE 4 -9 17 23 could be used to add atoms 4, 9 through 17, and 23 to the set of active atoms
during a Tinker calculation.

49
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8.2 Keywords Grouped by Functionality

Listed below are the available Tinker keywords sorted into groups by general function. The fol-
lowing section provides an alphabetical list containing each keyword, along with a more detailed
description of its action, possible keyword modifiers, and usage examples.

8.2.1 OUTPUT CONTROL KEYWORDS

ARCHIVE DCD-ARCHIVE DEBUG DIGITS ECHO EXIT-PAUSE NOVERSION OVERWRITE PRINTOUT

SAVE-CYCLE SAVE-FORCE SAVE-INDUCED SAVE-VELOCITY UNWRAP-COORDS VERBOSE WRAP-
COORDS WRITEOUT

8.2.2 FORCE FIELD SELECTION KEYWORDS

FORCEFIELD PARAMETERS

8.2.3 POTENTIAL FUNCTION SELECTION KEYWORDS

ANGANGTERM ANGLETERM BONDTERM CHARGETERM CHGDPLTERM DIPOLETERM EX-

TRATERM IMPROPTERM IMPTORSTERM METALTERM MPOLETERM NONBONDTERM OP-
BENDTERM OPDISTTERM PITORSTERM POLARIZETERM RESTRAINTERM RXNFIELDTERM SOL-
VATETERM STRBNDTERM STRTORTERM TORSIONTERM TORTORTERM UREYBRADTERM VA-
LENCETERM VDWTERM

8.2.4 POTENTIAL FUNCTION PARAMETER KEYWORDS

ANGANG ANGCFLUX ANGLE ANGLE3 ANGLE4 ANGLE5 ANGLEF ATOM BIOTYPE BNDCFLUX
BOND BOND3 BOND4 BOND5 CHARGE DIPOLE DIPOLE3 DIPOLE4 DIPOLE5 ELECTNEG EX-
CHPOL HBOND IMPROPER IMPTORS METAL MULTIPOLE OPBEND OPDIST PIATOM PIBOND
PITORS POLARIZE POLPAIR SOLUTE SOLVATE STRBND STRTORS TORSION TORSION4 TOR-
SION5 TORTOR UREYBRAD VDW VDW14 VDWPAIR

8.2.5 ENERGY UNIT CONVERSION KEYWORDS

ANGLEUNIT ANGANGUNIT BONDUNIT ELECTRIC IMPROPUNIT IMPTORUNIT OPBENDUNIT

OPDISTUNIT PITORSUNIT STRBNDUNIT STRTORUNIT TORSIONUNIT TORTORUNIT UREYUNIT

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8.2.6 LOCAL GEOMETRY FUNCTIONAL FORM KEYWORDS

ANGLE-CUBIC ANGLE-QUARTIC ANGLE-PENTIC ANGLE-SEXTIC BOND-CUBIC BOND-QUARTIC

BONDTYPE MM2-STRBND PISYSTEM UREY-CUBIC UREY-QUARTIC

8.2.7 VDW & REPULSION-DISPERSION FUNCTIONAL FORM KEYWORDS

A-EXPTERM B-EXPTERM C-EXPTERM DELTA-HALGREN DISP-12-SCALE DISP-13-SCALE DISP-

14-SCALE DISP-15-SCALE EPSILONRULE GAMMA-HALGREN GAUSSTYPE RADIUSRULE RA-
DIUSSIZE RADIUSTYPE VDW-12-SCALE VDW-13-SCALE VDW-14-SCALE VDW-15-SCALE VDW-
CORRECTION VDWINDEX VDWTYPE

8.2.8 ELECTROSTATICS FUNCTIONAL FORM KEYWORDS

CHG-12-SCALE CHG-13-SCALE CHG-14-SCALE CHG-15-SCALE CHG-BUFFER DIELECTRIC

DIRECT-11-SCALE DIRECT-12-SCALE DIRECT-13-SCALE DIRECT-14-SCALE EXCHANGE-POLAR
EXTERNAL-FIELD MPOLE-12-SCALE MPOLE-13-SCALE MPOLE-14-SCALE MPOLE-15-SCALE
MUTUAL-11-SCALE MUTUAL-12-SCALE MUTUAL-13-SCALE MUTUAL-14-SCALE POLAR-12-
SCALE POLAR-13-SCALE POLAR-14-SCALE POLAR-15-SCALE POLAR-ASPC POLAR-EPS POLAR-
SOR POLARIZATION REACTIONFIELD

8.2.9 NONBONDED CUTOFF KEYWORDS

CHG-CUTOFF CHG-TAPER CUTOFF DPL-CUTOFF DPL-TAPER HESS-CUTOFF LIGHTS MPOLE-

CUTOFF MPOLE-TAPER NEIGHBOR-GROUPS NEUTRAL-GROUPS POLYMER-CUTOFF TAPER
TRUNCATE VDW-CUTOFF VDW-TAPER

8.2.10 EWALD SUMMATION KEYWORDS

DPME-GRID DPME-ORDER EWALD EWALD-ALPHA EWALD-BOUNDARY EWALD-CUTOFF PME-

GRID PME-ORDER PPME-ORDER

8.2.11 CRYSTAL LATTICE & PERIODIC BOUNDARY KEYWORDS

A-AXIS B-AXIS C-AXIS ALPHA BETA DODECAHEDRON GAMMA NO-SYMMETRY OCTAHEDRON

SPACEGROUP X-AXIS Y-AXIS Z-AXIS

8.2. Keywords Grouped by Functionality 51

Tinker User's Guide

8.2.12 NEIGHBOR LIST KEYWORDS

CHG-LIST LIST-BUFFER MPOLE-LIST NEIGHBOR-LIST VDW-LIST

8.2.13 OPTIMIZATION KEYWORDS

ANGMAX CAPPA FCTMIN HGUESS INTMAX LBFGS-VECTORS MAXITER NEWHESS NEXTITER

SLOPEMAX STEEPEST-DESCENT STEPMAX STEPMIN

8.2.14 MOLECULAR DYNAMICS KEYWORDS

BEEMAN-MIXING DEGREES-FREEDOM INTEGRATOR REMOVE-INERTIA

8.2.15 THERMOSTAT & BAROSTAT KEYWORDS

ANISO-PRESSURE BAROSTAT COLLISION COMPRESS FRICTION FRICTION-SCALING TAU-

PRESSURE TAU-TEMPERATURE THERMOSTAT VOLUME-MOVE VOLUME-SCALE VOLUME-TRIAL

8.2.16 TRANSITION STATE KEYWORDS

DIVERGE GAMMAMIN REDUCE SADDLEPOINT

8.2.17 DISTANCE GEOMETRY KEYWORDS

TRIAL-DISTANCE TRIAL-DISTRIBUTION

8.2.18 VIBRATIONAL ANALYSIS KEYWORDS

IDUMP VIB-ROOTS VIB-TOLERANCE

8.2.19 IMPLICIT SOLVATION KEYWORDS

BORN-RADIUS CAVITY-PROBE DESCREEN-HYDROGEN DESCREEN-OFFSET GK-RADIUS GKC

GKR HCT-ELEMENT HCT-SCALE NECK-CORRECTION NODESCREEN ONION-PROBE SOLVENT-
PRESSURE SURFACE-TENSION TANH-CORRECTION

52 Chapter 8. Use of the Keyword Control File

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8.2.20 SURFACE AREA & VOLUME KEYWORDS

ALF-METHOD ALF-NOHYDRO ALF-SORT ALF-SOSGMP DELCX-EPS

8.2.21 POISSON-BOLTZMANN KEYWORDS

APBS-AGRID APBS-BCFL APBS-CGCENT APBS-CGRID APBS-CHGM APBS-DIME APBS-FGCENT

APBS-FGRID APBS-GCENT APBS-GRID APBS-ION APBS-MG-AUTO APBS-MG-MANUAL APBS-
PDIE APBS-RADII APBS-SDENS APBS-SDIE APBS-SMIN APBS-SRAD APBS-SRFM APBS-SWIN

8.2.22 MATHEMATICAL ALGORITHM KEYWORDS

FFT-PACKAGE RANDOMSEED

8.2.23 COMPUTER CONTROL KEYWORDS

CUDA-DEVICE OPENMP-THREADS

8.2.24 FREE ENERGY PERTURBATION KEYWORDS

CHG-LAMBDA DPL-LAMBDA LAMBDA LIGAND MPOLE-LAMBDA MUTATE POLAR-LAMBDA VDW-

ANNIHILATE VDW-LAMBDA

8.2.25 PARTIAL STRUCTURE KEYWORDS

ACTIVE GROUP GROUP-INTER GROUP-INTRA GROUP-MOLECULE GROUP-SELECT INACTIVE

8.2.26 CONSTRAINT & RESTRAINT KEYWORDS

BASIN ENFORCE-CHIRALITY RATTLE RATTLE-DISTANCE RATTLE-EPS RATTLE-LINE RATTLE-

ORIGIN RATTLE-PLANE RESTRAIN-ANGLE RESTRAIN-DISTANCE RESTRAIN-GROUPS
RESTRAIN-POSITION RESTRAIN-TORSION SPHERE WALL

8.2.27 ELECTROSTATIC POTENTIAL FITTING KEYWORDS

FIX-ATOM-DIPOLE FIX-CHGPEN FIX-DIPOLE FIX-MONOPOLE FIX-QUADRUPOLE POTENTIAL-

ATOMS POTENTIAL-FACTOR POTENTIAL-FIT POTENTIAL-OFFSET POTENTIAL-SHELLS
POTENTIAL-SPACING RESP-WEIGHT RESPTYPE TARGET-DIPOLE TARGET-QUADRUPOLE

8.2. Keywords Grouped by Functionality 53

Tinker User's Guide

8.2.28 VALENCE PARAMETER FITTING KEYWORDS

FIT-ANGLE FIT-BOND FIT-OPBEND FIT-STRBND FIT-TORSION FIT-UREY FIX-ANGLE FIX-BOND

FIX-OPBEND FIX-STRBND FIX-TORSION FIX-UREY

8.2.29 POTENTIAL SMOOTHING KEYWORDS

DEFORM DIFFUSE-CHARGE DIFFUSE-TORSION DIFFUSE-VDW SMOOTHING

8.3 Description of Individual Keywords

The following is an alphabetical list of the Tinker keywords along with a brief description of the
action of each keyword and required or optional parameters that can be used to extend or mod-
ify each keyword. The format of possible modifiers, if any, is shown in brackets following each
keyword.
A-AXIS [real]
Sets the value of the a-axis length for a crystal unit cell, or, equivalently, the X-axis length for
a periodic box. The length value in Angstroms is provided following the keyword. Equivalent
to the X-AXIS keyword.
A-EXPTERM [real]
Sets the value of the “A” premultiplier term in the Buckingham van der Waals function, i.e.,
the value of A in the formula Evdw = epsilon * { A exp[-B(Ro/R)] - C (Ro/R)6 }.
ACTIVE [integer list]
Sets the list of active atoms during a Tinker computation. Individual potential energy terms
are computed when at least one atom involved in the term is active. For Cartesian space cal-
culations, active atoms are those allowed to move. For torsional space calculations, rotations
are allowed when all atoms on one side of the rotated bond are active. Multiple ACTIVE
lines can be present in the keyfile and are treated cumulatively. On each line the keyword
can be followed by one or more atom numbers or atom ranges. The presence of any ACTIVE
keyword overrides any INACTIVE keywords in the keyfile.
ACTIVE-SPHERE [4 reals, or 1 integer & 1 real]
Provides an alternative to the ACTIVE and INACTIVE keywords for specification of subsets of
active atoms. If four real number modifiers are provided, the first three are taken as X-, Y-
and Z-coordinates and the fourth is the radius of a sphere centered at these coordinates. In
this case, all atoms within the sphere at the start of the calculation are active throughout the
calculation, while all other atoms are inactive. Similarly if one integer and real number are
given, an “active” sphere with radius set by the real is centered on the system atom with atom
number given by the integer modifier. Multiple SPHERE keyword lines can be present in a
single keyfile, and the list of active atoms specified by the spheres is cumulative.
ALF-METHOD [SINGLE / MULTI; & integer]
Sets the AlphaMol code base and parallelization for surface area and volume calculations.The
SINGLE option inforces use of the single-threaded AlphaMol1 method, while the MULTI op-
tion selects the multi-threaded AlphaMol2 code base. The MULTI option takes an optional

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additional integer that specifies the number of OpenMP threads to use. The default value in
the absence of the ALF-METHOD keyword is SINGLE, and the default number of threads is
one.
ALF-NOHYDRO
Causes hydrogen atoms to be omitted from surface area and volume calculations with the Al-
phaMol code within Tinker. The default value in the absence of the ALF-NOHYDRO keyword
is to include all atoms when invoking AlphaMol.
ALF-SORT [NONE / SORT3D / BRIO / SPLIT / KDTREE]
Controls use of specialized sorting or spatial decomposition algorithms during AlphaMol sur-
face area and volume calculations. The following option then selects the method to be used.
The default in the absence of the ALF-SORT keyword is the NONE option, which avoids use
of any specialized sorting method.
ALF-SOSGMP
Turns on use of the SOS procedure and GMP library calls for degenerate cases such as linear,
planar or symmetric systems during AlphaMol surface area and volume calculations. The
default in the absence of the ALF-SOSGMP keyword is to use standard precision arithmetic in
place of special SOS code and GMP library calls.
ALPHA [real]
Sets the value of the alpha angle of a crystal unit cell, i.e., the angle between the b-axis and
c-axis of a unit cell, or, equivalently, the angle between the Y-axis and Z-axis of a periodic box.
The default value in the absence of the ALPHA keyword is 90 degrees.
ANGANG [1 integer & 3 reals]
Provides the values for a single angle-angle cross term potential parameter. The integer mod-
ifier is the atom class of the central atom in the coupled angles. The real number modifiers
give the force constant values for individual angles with 0, 1 or 2 terminal hydrogen atoms,
respectively. The default units for the force constant are kcal/mole/radian^2, but this can
be controlled via the ANGANGUNIT keyword.
ANGANGTERM [NONE / ONLY]
Controls use of the angle-angle cross term potential energy. In the absence of a modifying
option, this keyword turns on use of the potential. The NONE option turns off use of this
potential energy term. The ONLY option turns off all potential energy terms except for this
one.
ANGANGUNIT [real]
Sets the scale factor needed to convert the energy value computed by the angle-angle cross
term potential into units of kcal/mole. The correct value is force field dependent and typically
provided in the header of the master force field parameter file. The default of (Pi/180)^2 =
0.0003046 is used, if the ANGANGUNIT keyword is not given in the force field parameter file
or the keyfile.
ANGCFLUX [3 integers & 4 reals]
Provides the values for a single angle bending charge flux parameter. The integer modifiers
give the atom class numbers for the three kinds of atoms involved in the angle which is to be
defined. The first two real modifiers are the angle deviation scale factors for the two included
bonds in electrons/radian. The second two modifiers are the bond deviation scale factors for
the two included bonds in electrons/Angstrom.

8.3. Description of Individual Keywords 55

Tinker User's Guide

ANGLE [3 integers & 4 reals]

Provides the values for a single bond angle bending parameter. The integer modifiers give
the atom class numbers for the three kinds of atoms involved in the angle which is to be
defined. The real number modifiers give the force constant value for the angle and up to
three ideal bond angles in degrees. In most cases only one ideal bond angle is given, and
that value is used for all occurrences of the specified bond angle. If all three ideal angles
are given, the values apply when the central atom of the angle is attached to 0, 1 or 2
additional hydrogen atoms, respectively. This “hydrogen environment” option is provided
to implement the corresponding feature of Allinger’s MM force fields. The default units for
the force constant are kcal/mole/radian^2, but this can be controlled via the ANGLEUNIT
keyword.
ANGLE-CUBIC [real]
Sets the value of the cubic term in the Taylor series expansion form of the bond angle bending
potential energy. The real number modifier gives the value of the coefficient as a multiple of
the quadratic coefficient. This term multiplied by the angle bending energy unit conversion
factor, the force constant, and the cube of the deviation of the bond angle from its ideal value
gives the cubic contribution to the angle bending energy. The default value in the absence of
the ANGLE-CUBIC keyword is zero; i.e., the cubic angle bending term is omitted.
ANGLE-PENTIC [real]
Sets the value of the fifth power term in the Taylor series expansion form of the bond angle
bending potential energy. The real number modifier gives the value of the coefficient as a
multiple of the quadratic coefficient. This term multiplied by the angle bending energy unit
conversion factor, the force constant, and the fifth power of the deviation of the bond angle
from its ideal value gives the pentic contribution to the angle bending energy. The default
value in the absence of the ANGLE-PENTIC keyword is zero; i.e., the pentic angle bending
term is omitted.
ANGLE-QUARTIC [real]
Sets the value of the quartic term in the Taylor series expansion form of the bond angle
bending potential energy. The real number modifier gives the value of the coefficient as a
multiple of the quadratic coefficient. This term multiplied by the angle bending energy unit
conversion factor, the force constant, and the forth power of the deviation of the bond angle
from its ideal value gives the quartic contribution to the angle bending energy. The default
value in the absence of the ANGLE-QUARTIC keyword is zero; i.e., the quartic angle bending
term is omitted.
ANGLE-SEXTIC [real]
Sets the value of the sixth power term in the Taylor series expansion form of the bond angle
bending potential energy. The real number modifier gives the value of the coefficient as a
multiple of the quadratic coefficient. This term multiplied by the angle bending energy unit
conversion factor, the force constant, and the sixth power of the deviation of the bond angle
from its ideal value gives the sextic contribution to the angle bending energy. The default
value in the absence of the ANGLE-SEXTIC keyword is zero; i.e., the sextic angle bending
term is omitted.
ANGLE3 [3 integers & 4 reals]
Provides the values for a single bond angle bending parameter specific to atoms in 3-
membered rings. The integer modifiers give the atom class numbers for the three kinds

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of atoms involved in the angle which is to be defined. The real number modifiers give the
force constant value for the angle and up to three ideal bond angles in degrees. If all three
ideal angles are given, the values apply when the central atom of the angle is attached to
0, 1 or 2 additional hydrogen atoms, respectively. The default units for the force constant
are kcal/mole/radian^2, but this can be controlled via the ANGLEUNIT keyword. If any
ANGLE3 keywords are present, either in the master force field parameter file or the keyfile,
then Tinker requires that special ANGLE3 parameters be given for all angles in 3-membered
rings. In the absence of any ANGLE3 keywords, standard ANGLE parameters will be used for
bonds in 3-membered rings.
ANGLE4 [3 integers & 4 reals]
Provides the values for a single bond angle bending parameter specific to atoms in 4-
membered rings. The integer modifiers give the atom class numbers for the three kinds
of atoms involved in the angle which is to be defined. The real number modifiers give the
force constant value for the angle and up to three ideal bond angles in degrees. If all three
ideal angles are given, the values apply when the central atom of the angle is attached to
0, 1 or 2 additional hydrogen atoms, respectively. The default units for the force constant
are kcal/mole/radian^2, but this can be controlled via the ANGLEUNIT keyword. If any
ANGLE4 keywords are present, either in the master force field parameter file or the keyfile,
then Tinker requires that special ANGLE4 parameters be given for all angles in 4-membered
rings. In the absence of any ANGLE4 keywords, standard ANGLE parameters will be used for
bonds in 4-membered rings.
ANGLE5 [3 integers & 4 reals]
Provides the values for a single bond angle bending parameter specific to atoms in 5-
membered rings. The integer modifiers give the atom class numbers for the three kinds
of atoms involved in the angle which is to be defined. The real number modifiers give the
force constant value for the angle and up to three ideal bond angles in degrees. If all three
ideal angles are given, the values apply when the central atom of the angle is attached to
0, 1 or 2 additional hydrogen atoms, respectively. The default units for the force constant
are kcal/mole/radian^2, but this can be controlled via the ANGLEUNIT keyword. If any
ANGLE5 keywords are present, either in the master force field parameter file or the keyfile,
then Tinker requires that special ANGLE5 parameters be given for all angles in 5-membered
rings. In the absence of any ANGLE5 keywords, standard ANGLE parameters will be used for
bonds in 5-membered rings.
ANGLEF [3 integers & 3 reals]
Provides the values for a single bond angle bending parameter for a SHAPES-style Fourier
potential function. The integer modifiers give the atom class numbers for the three kinds of
atoms involved in the angle which is to be defined. The real number modifiers give the force
constant value for the angle, the angle shift in degrees, and the periodicity value. Note that
the force constant should be given as the “harmonic” value and not the native Fourier value.
The default units for the force constant are kcal/mole/radian^2, but this can be controlled
via the ANGLEUNIT keyword.
ANGLEP [3 integers & 3 reals]
Provides the values for a single projected in-plane bond angle bending parameter. The integer
modifiers give the atom class numbers for the three kinds of atoms involved in the angle
which is to be defined. The real number modifiers give the force constant value for the angle
and up to two ideal bond angles in degrees. In most cases only one ideal bond angle is

8.3. Description of Individual Keywords 57

Tinker User's Guide

given, and that value is used for all occurrences of the specified bond angle. If all two ideal
angles are given, the values apply when the central atom of the angle is attached to 0 or
1 additional hydrogen atoms, respectively. This “hydrogen environment” option is provided
to implement the corresponding feature of Allinger’s MM force fields. The default units for
the force constant are kcal/mole/radian2, but this can be controlled via the ANGLEUNIT
keyword.
ANGLETERM [NONE / ONLY]
Controls use of the bond angle bending potential energy term. In the absence of a modifying
option, this keyword turns on use of the potential. The NONE option turns off use of this
potential energy term. The ONLY option turns off all potential energy terms except for this
one.
ANGLEUNIT [real]
Sets the scale factor needed to convert the energy value computed by the bond angle bending
potential into units of kcal/mole. The correct value is force field dependent and typically pro-
vided in the header of the master force field parameter file. The default value of (Pi/180)^2
= 0.0003046 is used, if the ANGLEUNIT keyword is not given in the force field parameter file
or the keyfile.
ANGMAX [real]
Set the maximum permissible angle between the current optimization search direction and
the negative of the gradient direction. If this maximum angle value is exceeded, the op-
timization routine will note an error condition and may restart from the steepest descent
direction. The default value in the absence of the ANGMAX keyword is usually 88 degrees for
conjugate gradient methods and 180 degrees (i.e., ANGMAX is disabled) for variable metric
optimizations.
ANGTORS [4 integers & 6 reals]
Provides the values for a single bond angle bending-torsional angle parameter. The integer
modifiers give the atom class numbers for the four kinds of atoms involved in the torsion and
its contained angles. The real number modifiers give the force constant values for both angles
coupled with 1-, 2- and 3-fold torsional terms. The default units for the force constants are
kcal/mole/radian, but this can be controlled via the ANGTORUNIT keyword.
ANGTORTERM [NONE / ONLY]
Controls use of the angle bending-torsional angle cross term. In the absence of a modifying
option, this keyword turns on use of the potential. The NONE option turns off use of this
potential energy term. The ONLY option turns off all potential energy terms except for this
one.
ANGTORUNIT [real]
Sets the scale factor needed to convert the energy value computed by the angle bending-
torsional angle cross term into units of kcal/mole. The correct value is force field dependent
and typically provided in the header of the master force field parameter file. The default value
of (Pi/180) = 0.0174533 is used, if the ANGTORUNIT keyword is not given in the force field
parameter file or the keyfile.
ANISO-PRESSURE
Invokes use of full anisotropic pressure during dynamics simulations. When using this option,
the three axis lengths and axis angles vary separately in response to the pressure tensor. The

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default, in the absence of the keyword, is isotropic pressure based on the average of the
diagonal of the pressure tensor.
APBS-AGRID [3 reals]
Sets grid spacing in Angstroms along the X-, Y- and Z-axes which are passed on to the APBS
interface for use in Poisson-Boltzmann calculations.
APBS-BCFL [ZERO / SDH / MDH]
Chooses the type of initialization conditions to be used at the coarse grid boundary when
performing Poisson-Boltzmann calculations. The ZERO modifier denotes a zero potential at
the boundary, while SDH and MDH are single and multiple Debye-Huckel conditions. The
default setting in the absence of the BCFL keyword is to use the MDH boundary conditions.
APBS-CGCENT [3 reals]
Sets the coarse grid center as X-, Y- and Z-axis coordinates for an APBS Poisson-Boltzmann
calculation when using a “focusing” calculation as activated via the APBS-MG-AUTO keyword.
APBS-CGRID [3 reals]
Sets the coarse grid dimensions along the X-, Y- and Z-axes for an APBS Poisson-Boltzmann
calculation when using a “focusing” calculation as activated via the APBS-MG-AUTO keyword.
APBS-CHGM [SPL0 / SPL2 / SPL4]
Specifies the model used to map the electrostatic model onto grid points during APBS Poisson-
Boltzmann calculations. The SPL0 modifier uses linear splines to move charges to the nearest
grid point. The SPL2 and SPL4 models use a cubic spline surface and a 7th order polynomial
to spread to two and three layers of grid points, respectively. The default in the absence of
the APBS-CHGM keyword is to use the SPL4 model.
APBS-DIME [3 integers]
Specifies the number of grid points along the X-, Y- and Z-axes for APBS Poisson-Boltzmann
calculations. This keyword gives final, custom control over the grid dimensions that are
usually set via the APBS-GRID keyword. When using traceless atomic quadrupole moments,
all grid dimensions will be forced to be equal.
APBS-FGCENT [3 reals]
Sets the fine grid center as X-, Y- and Z-axis coordinates for an APBS Poisson-Boltzmann
calculation when using a “focusing” calculation as activated via the APBS-MG-AUTO keyword.
APBS-FGRID [3 reals]
Sets the fine grid dimensions along the X-, Y- and Z-axes for an APBS Poisson-Boltzmann
calculation when using a “focusing” calculation as activated via the APBS-MG-AUTO keyword.
APBS-GCENT [3 reals]
Sets grid dimensions along the X-, Y- and Z-axes which are passed on to the Tinker APBS
interface for use in Poisson-Boltzmann calculations.
APBS-GRID [3 integers]
Sets the number of grid points along the X-, Y- and Z-axes when performing an APBS Poisson-
Boltzmann calculation. The default values in the absence of the APBS-GRID keyword are
chosen as the nearest integers that provide a 0.5 Angstrom grid spacing along each axis.
When using traceless atomic quadrupole moments, all grid dimensions will be forced to be
equal.

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Tinker User's Guide

APBS-ION [3 reals]
Specifies the mobile ion concentration for use during APBS Poisson-Boltzmann calculations.
The real modifiers are the charge of the ion species in electrons, the molar ion concentration,
and the radius in Angstroms of the ion species. The default in the absence of the APBS-ION
keyword is to not include any mobile ions via setting the concentration to zero.
APBS-MG-AUTO
Specifies a “focusing” multigrid APBS Poisson-Boltzmann calculation where a series of single-
point calculations are used to successively zoom in on a region of interest in a system. It
is basically an automated version of the default MG-MANUAL mode, which is designed for
easier use.
APBS-MG-MANUAL
Specifies a manually configured single-point multigrid APBS Poisson-Boltzmann calculation
without focusing or additional refinement. This mode offers the most control of APBS param-
eters to the user. This is the default mode for APBS calculations unless the APBS-MG-MANUAL
keyword is present.
APBS-PDIE [real]
Specifies the dielectric constant of the solute molecule for APBS Poisson-Boltzmann calcula-
tions. This is often a value between 2 and 20, where lower values consider only electronic
polarization and higher values account for additional polarization due to intramolecular mo-
tion. The default in the absence of the APBS-PDIE keyword is to set the solute dielectric
constant to 1.0.
APBS-RADII [VDW / MACROMODEL / BONDI / TOMASI]
Specifies the atomic radii values to be used during APBS Poisson-Boltzmann calculations. The
default in the absence o the APBS-RADII keyword is to use BONDI radii.
APBS-SDENS [real]
Sets the number of quadrature points per square Angstrom to use in surface area terms dur-
ing APSB Poisson-Boltzmann calculations. The default in the absence of the APBS-SDENS
keyword is to use a value of 10.0, although this keyword is ignored it APBS-SRAD is zero.
APBS-SDIE [real]
Specifies the dielectric constant of the solvent for APBS Poisson-Boltzmann calculations. Bulk
water is usually modeled with a dielectric constant of 78 to 80. The default in the absence of
the APBS-SDIE keyword is to set the solvent dielectric constant to 78.3.
APBS-SMIN [real]
Sets an offset buffer distance in Angstroms to be added to the width of the solute molecule
in determination of the grid dimension and spacing during an APBS Poisson-Boltzmann cal-
culation. The default in the absence of the APBS-SMIN keyword is to use a value of 3.0
Angstroms.
APBS-SRAD [real]
Provides the radius in Angstroms of solvent molecules to be used during APBS Poisson-
Boltzmann calculations. This value is usually set to 1.4 for a water-like molecular surface,
and set to zero for a van der Waals surface. The default in the absence of the APBS-SRAD
keyword is to use a value of 0.0 Angstroms.
APBS-SRFM [MOL / SMOL / SPL2 / SPL4]

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Specifies the model used to construct the dielectric and ion-accessibility coefficients during
APBS Poisson-Boltzmann calculations. The MOL modifier sets the dielectric coefficient based
on the molecular surface, while SMOL uses a smoothed molecular surface. The SPL2 and
SPL4 models use a cubic spline surface and a 7th order polynomial, respectively. The default
in the absence of the APBS-SRFM keyword is to use the MOL model.
APBS-SWIN [real]
Specifies the spline window width in Angstroms for surface definitions during APBS Poisson-
Boltzmann calculations. The default in the absence of the APBS-SWIN keyword is to use a
value of 0.3 Angstroms.
ARCHIVE
Causes Tinker molecular dynamics-based programs to write trajectory frames directly to a
single plain-text archive file with the .arc format. If an archive file already exists at the start
of the calculation, then the newly generated trajectory is appended to the end of the existing
file. The ARCHIVE behavior is the default and is used in the absence of this keyword unless
the NO-ARCHIVE or ARCHIVE-DCD keywords are present.
ATOM [2 integers, name, quoted string, integer, real & integer]
Provides the values needed to define a single force field atom type. The first two integer
modifiers denote the atom type and class numbers. If the type and class are identical, only a
single integer value is required. The next modifier is a three-character atom name, followed
by an 24-character or less atom description contained in single quotes. The next two modifiers
are the atomic number and atomic mass. The final integer modifier is the “valence” of the
atom, defined as the expected number of attached or bonded atoms.
AUX-TAUTEMP [real]
Sets the coupling time in picoseconds for the temperature bath coupling used to control the
auxiliary thermostat temperature value when using the iELSCF induced dipole method. A
default value of 0.1 is used for AUX-TAUTEMP in the absence of the keyword.
AUX-TEMP [real]
Sets the target temperature used for the auxiliary control variable when using the iELSCF
induced dipole method. A default value of 100000.0 is used for AUX-TEMP in the absence of
the keyword.
B-AXIS [real]
Sets the value of the b-axis length for a crystal unit cell, or, equivalently, the Y-axis length
for a periodic box. The length value in Angstroms is provided following the keyword. If the
keyword is absent, the b-axis length is set equal to the a-axis length. Equivalent to the Y-AXIS
keyword.
B-EXPTERM [real]
Sets the value of the “B” exponential factor in the Buckingham van der Waals function, i.e.,
the value of B in the formula Evdw = epsilon * { A exp[-B(Ro/R)] - C (Ro/R)6 }.
BAROSTAT [BERENDSEN / BUSSI / NOSE-HOOVER / MONTECARLO]
Selects a barostat algorithm for use during molecular dynamics. At present the options in-
clude three virial-based methods, in addition to a Monte Carlo barostat. The default in the
absence of the BAROSTAT keyword is to use the BERENDSEN algorithm.
BASIN [2 reals]

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Presence of this keyword turns on a “basin” restraint potential function that serves to drive
the system toward a compact structure. The actual function is a Gaussian of the form Ebasin
= epsilon * A exp[-B R^2], summed over all pairs of atoms where R is the distance between
atoms. The A and B values are the depth and width parameters given as modifiers to the
BASIN keyword. This potential is currently used to control the degree of expansion during
potential energy smooth procedures through the use of shallow, broad basins.
BEEMAN-MIXING [integer]
Sets the “mixing” coefficient between old and new forces in position and velocity updates
when using the Beeman integrator. The original algorithm of Beeman uses a value of 6. The
default value in the absence of the BEEMAN-MIXING keyword is to use 8, which corresponds
to the “Better Beeman” algorithm proposed by Bernie Brooks.
BETA [real]
Sets the value of the ? angle of a crystal unit cell, i.e., the angle between the a-axis and c-axis
of a unit cell, or, equivalently, the angle between the X-axis and Z-axis of a periodic box. The
default value in the absence of the BETA keyword is to set the beta angle equal to the alpha
angle as given by the keyword ALPHA.
BIOTYPE [integer, name, quoted string & integer]
Provides the values to define the correspondence between a single biopolymer atom type and
its force field atom type.
BOND [2 integers & 2 reals]
Provides the values for a single bond stretching parameter. The integer modifiers give the
atom class numbers for the two kinds of atoms involved in the bond which is to be defined.
The real number modifiers give the force constant value for the bond and the ideal bond
length in Angstroms. The default units for the force constant are kcal/mole/Ang^2, but this
can be controlled via the BONDUNIT keyword.
BOND-CUBIC [real]
Sets the value of the cubic term in the Taylor series expansion form of the bond stretching
potential energy. The real number modifier gives the value of the coefficient as a multiple of
the quadratic coefficient. This term multiplied by the bond stretching energy unit conversion
factor, the force constant, and the cube of the deviation of the bond length from its ideal value
gives the cubic contribution to the bond stretching energy. The default value in the absence
of the BOND-CUBIC keyword is zero; i.e., the cubic bond stretching term is omitted.
BOND-QUARTIC [real]
Sets the value of the quartic term in the Taylor series expansion form of the bond stretching
potential energy. The real number modifier gives the value of the coefficient as a multiple of
the quadratic coefficient. This term multiplied by the bond stretching energy unit conversion
factor, the force constant, and the forth power of the deviation of the bond length from its
ideal value gives the quartic contribution to the bond stretching energy. The default value in
the absence of the BOND-QUARTIC keyword is zero; i.e., the quartic bond stretching term is
omitted.
BOND3 [2 integers & 2 reals]
Provides the values for a single bond stretching parameter specific to atoms in 3-membered
rings. The integer modifiers give the atom class numbers for the two kinds of atoms involved
in the bond which is to be defined. The real number modifiers give the force constant value

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for the bond and the ideal bond length in Angstroms. The default units for the force constant
are kcal/mole/Ang^2, but this can be controlled via the BONDUNIT keyword. If any BOND3
keywords are present, either in the master force field parameter file or the keyfile, then Tinker
requires that special BOND3 parameters be given for all bonds in 3-membered rings. In the
absence of any BOND3 keywords, standard BOND parameters will be used for bonds in 3-
membered rings.
BOND4 [2 integers & 2 reals]
Provides the values for a single bond stretching parameter specific to atoms in 4-membered
rings. The integer modifiers give the atom class numbers for the two kinds of atoms involved
in the bond which is to be defined. The real number modifiers give the force constant value
for the bond and the ideal bond length in Angstroms. The default units for the force constant
are kcal/mole/Ang^2, but this can be controlled via the BONDUNIT keyword. If any BOND4
keywords are present, either in the master force field parameter file or the keyfile, then Tinker
requires that special BOND4 parameters be given for all bonds in 4-membered rings. In the
absence of any BOND4 keywords, standard BOND parameters will be used for bonds in 4-
membered rings
BOND5 [2 integers & 2 reals]
Provides the values for a single bond stretching parameter specific to atoms in 5-membered
rings. The integer modifiers give the atom class numbers for the two kinds of atoms involved
in the bond which is to be defined. The real number modifiers give the force constant value
for the bond and the ideal bond length in Angstroms. The default units for the force constant
are kcal/mole/Ang^2, but this can be controlled via the BONDUNIT keyword. If any BOND5
keywords are present, either in the master force field parameter file or the keyfile, then Tinker
requires that special BOND5 parameters be given for all bonds in 5-membered rings. In the
absence of any BOND5 keywords, standard BOND parameters will be used for bonds in 5-
membered rings
BONDTERM [NONE / ONLY]
Controls use of the bond stretching potential energy term. In the absence of a modifying
option, this keyword turns on use of the potential. The NONE option turns off use of this
potential energy term. The ONLY option turns off all potential energy terms except for this
one.
BONDTYPE [HARMONIC / MORSE]
Chooses the functional form of the bond stretching potential. The HARMONIC option selects a
Taylor series expansion containing terms from harmonic through quartic. The MORSE option
selects a Morse potential fit to the ideal bond length and stretching force constant parameter
values. The default is to use the HARMONIC potential.
BONDUNIT [real]
Sets the scale factor needed to convert the energy value computed by the bond stretching
potential into units of kcal/mole. The correct value is force field dependent and typically
provided in the header of the master force field parameter file. The default value of 1.0 is
used, if the BONDUNIT keyword is not given in the force field parameter file or the keyfile.
BORN-RADIUS [ONION / STILL / HCT / OBC / ACE / GRYCUK / PERFECT]
Sets the algorithm used for computation of Born radii. The default behavior is to set BORN-
RADIUS the same as the SOLVATE keyword, when possible. For Generalized Kirkwood mod-
els, the default value is set to GRYCUK.

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C-AXIS [real]
Sets the value of the C-axis length for a crystal unit cell, or, equivalently, the Z-axis length
for a periodic box. The length value in Angstroms is provided following the keyword. If the
keyword is absent, the C-axis length is set equal to the A-axis length. Equivalent to the Z-AXIS
keyword.
C-EXPTERM [real]
Sets the value of the “C” dispersion multiplier in the Buckingham van der Waals function, i.e.,
the value of C in the formula Evdw = epsilon * { A*exp[-B(Ro/R)] - C*(Ro/R)^6 }.
CAPPA [real]
Sets the normal termination criterion for the line search phase of Tinker optimization rou-
tines. The line search exits successfully if the ratio of the current gradient projection on the
line to the projection at the start of the line search falls below the value of CAPPA. A default
value of 0.1 is used in the absence of the CAPPA keyword.
CAVITY-PROBE [real]
Sets the value in Angstroms of the solvent probe radius to be used in computing solvent
accessible surface area and excluded volume as part of the nonpolar cavitation term of an
implicit solvent model. A default value of 1.4 is used in the absence of the CAVITY-PROBE
keyword.
CHARGE [1 integer & 1 real]
Provides a value for a single atomic partial charge electrostatic parameter. The integer modi-
fier, if positive, gives the atom type number for which the charge parameter is to be defined.
Note that charge parameters are given for atom types, not atom classes. If the integer modi-
fier is negative, then the parameter value to follow applies only to the individual atom whose
atom number is the negative of the modifier. The real number modifier gives the values of
the atomic partial charge in electrons.
CHARGE-CUTOFF [real]
Sets the cutoff distance value in Angstroms for charge-charge electrostatic potential energy
interactions. The energy for any pair of sites beyond the cutoff distance will be set to zero.
Other keywords can be used to select a smoothing scheme near the cutoff distance. The
default cutoff distance in the absence of the CHG-CUTOFF keyword is infinite for nonperiodic
systems and 9.0 for periodic systems.
CHARGE-LIST
Turns on the use of pairwise neighbor lists for partial charge electrostatics. This method will
yield identical energetic results to the standard double loop method.
CHARGE-TAPER [real]
Modifies the cutoff window for charge-charge electrostatic potential energy interactions. It
is similar in form and action to the TAPER keyword, except that its value applies only to the
charge-charge potential. The default value in the absence of the CHG-TAPER keyword is to
begin the cutoff window at 0.65 of the corresponding cutoff distance.
CHARGETERM [NONE / ONLY]
Controls use of the charge-charge potential energy term between pairs of atomic partial
charges. In the absence of a modifying option, this keyword turns on use of the potential.
The NONE option turns off use of this potential energy term. The ONLY option turns off all
potential energy terms except for this one.

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CHARGETRANSFER [SEPARATE / COMBINED]

Chooses the formulation used for the charge transfer potential energy function. The SEP-
ARATE method includes separate terms for charge transfer in both directions between two
atomic sites. The COMBINED model uses a single term to account for the total charge trans-
fer interaction between two sites. The default value in the absence of the CHARGETRANSFER
keyword is to use the SEPARATE expression to compute the charge transfer potential.
CHG-11-SCALE [real]
Provides a multiplicative scale factor that is applied to charge-charge electrostatic interactions
between self-atoms. These interactions are usually to be ignored, but this value is used in
certain cases involving infinite polymers or atoms using the same “neighbor generating” site.
The default value of 0.0 is used, if the CHG-11-SCALE keyword is not given in either the
parameter file or the keyfile.
CHG-12-SCALE [real]
Provides a multiplicative scale factor that is applied to charge-charge electrostatic interactions
between 1-2 connected atoms, i.e., atoms that are directly bonded. The default value of 0.0
is used, if the CHG-12-SCALE keyword is not given in either the parameter file or the keyfile.
CHG-13-SCALE [real]
Provides a multiplicative scale factor that is applied to charge-charge electrostatic interactions
between 1-3 connected atoms, i.e., atoms separated by two covalent bonds. The default value
of 0.0 is used, if the CHG-13-SCALE keyword is not given in either the parameter file or the
keyfile.
CHG-14-SCALE [real]
Provides a multiplicative scale factor that is applied to charge-charge electrostatic interactions
between 1-4 connected atoms, i.e., atoms separated by three covalent bonds. The default
value of 1.0 is used, if the CHG-14-SCALE keyword is not given in either the parameter file
or the keyfile.
CHG-15-SCALE [real]
Provides a multiplicative scale factor that is applied to charge-charge electrostatic interactions
between 1-5 connected atoms, i.e., atoms separated by four covalent bonds. The default value
of 1.0 is used, if the CHG-15-SCALE keyword is not given in either the parameter file or the
keyfile.
CHG-BUFFER [real]
Specifies a fixed value which is added to the distance between pairs of atoms when applying
Coulomb’s law in the computation of partial charge electrostatic interactions. The default
value of 0.0, which disables the use of the charge buffer mechanism, is used in the absence
of the CHG-BUFFER keyword.
CHGDPLTERM [NONE / ONLY]
Controls use of the charge-dipole potential energy term between atomic partial charges and
bond dipoles. In the absence of a modifying option, this keyword turns on use of the potential.
The NONE option turns off use of this potential energy term. The ONLY option turns off all
potential energy terms except for this one.
CHGFLXTERM [NONE / ONLY]
Controls use of the charge flux potential energy term. In the absence of a modifying option,
this keyword turns on use of the potential. The NONE option turns off use of this potential

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Tinker User's Guide

energy term. The ONLY option turns off all potential energy terms except for this one, though
electrostatic terms must also be active for charge flux to be computed.
CHGPEN [1 integer & 2 reals]
Provides values for a single charge penetration parameter. The integer modifier, if positive,
gives the atom class number for which the charge penetration is to be defined. If the integer
modifier is negative, then the parameter values to follow apply only to the individual atom
whose atom number is the negative of the modifier. The real number modifiers give the
number of core electrons for the atomic site and the “alpha” exponent controlling the stregth
of the charge penetration effect.
CHGTRN [1 integer & 2 reals]
Provides values for a single charge transfer parameter. The integer modifier, if positive, gives
the atom class number for which the charge transfer is to be defined. If the integer modifier
is negative, then the parameter values to follow apply only to the individual atom whose
atom number is the negative of the modifier. The real number modifiers give the charge to
be transferred for the atomic site and the “alpha” exponent controlling the damping of the
charge transfer.
CHGTRN-CUTOFF [real]
Sets the cutoff distance value in Angstroms for charge transfer potential energy interactions.
The energy for any pair of sites beyond the cutoff distance will be set to zero. Other keywords
can be used to select a smoothing scheme near the cutoff distance. The default cutoff distance
in the absence of the CHGTRN-CUTOFF keyword is 6.0 Angstroms.
CHGTRN-TAPER [real]
Modifies the cutoff window for charge transfer potential energy interactions. It is similar
in form and action to the TAPER keyword, except that its value applies only to the charge
transfer potential. The default value in the absence of the CHGTRN-TAPER keyword is to
begin the cutoff window at 0.9 of the corresponding cutoff distance.
CHGTRNTERM [NONE / ONLY]
Controls use of the charge transfer potential energy term. In the absence of a modifying
option, this keyword turns on use of the potential. The NONE option turns off use of this
potential energy term. The ONLY option turns off all potential energy terms except for this
one.
COLLISION [real]
Sets the value of the random collision frequency used in the Andersen stochastic collision
dynamics thermostat. The supplied value has units of fs-1 atom-1 and is multiplied internal
to Tinker by the time step in fs and N^2/3 where N is the number of atoms. The default value
used in the absence of the COLLISION keyword is 0.1 which is appropriate for many systems
but may need adjustment to achieve adequate temperature control without perturbing the
dynamics.
COMPRESS [real]
Sets the value of the bulk solvent isothermal compressibility in 1/Atm for use during pressure
computation and scaling in molecular dynamics computations. The default value used in
the absence of the COMPRESS keyword is 0.000046, appropriate for water. This parameter
serves as a scale factor for the Groningen-style pressure bath coupling time, and its exact
value should not be of critical importance.

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CUDA-DEVICE [integer]
Sets the device number of the NVIDIA GPU to be used for calculations with CUDA-enabled
versions of Tinker, such as Tinker9, Tinker-OpenMM and Tinker-HP. The CUDA-capable de-
vices are numbered internally by the system with consecutive integers, starting with 0 for the
first device. An the absence of the CUDA-DEVICE keyword, most of the Tinker GPU programs
will attempt to use the fastest GPU that is not currently performing a calculation.
CUTOFF [real]
Sets the cutoff distance value for all nonbonded potential energy interactions. The energy for
any of the nonbonded potentials of a pair of sites beyond the cutoff distance will be set to
zero. Other keywords can be used to select a smoothing scheme near the cutoff distance, or
to apply different cutoff distances to various nonbonded energy terms.
D-EQUALS-P
Forces the direct induction (“D”) scale factors to be set equal to the polarization energy (“P”)
scale factors during computation of induced dipoles and the polarization potential energy. In
the absence of the D-EQUALS-P keyword, these two sets of scale factors are independent and
are allowed to be different.
DCD-ARCHIVE
Causes Tinker molecular dynamics-based programs to write trajectory frames directly to a
single binary archive file in the CHARMM/XPLOR DCD format compatible with VMD and
other programs, and having the .dcd extension. If a DCD archive file already exists at the
start of the calculation, then the newly generated trajectory is appended to the end of the
existing file. The default in the absence of this keyword is the ARCHIVE behavior or writing
a single formatted trajectory file with the .arc extension.
DEBUG
Turns on printing of detailed information and intermediate values throughout the progress of
a Tinker computation; not recommended for use with large structures or full potential energy
functions since a summary of every individual interaction will usually be output.
DEFORM [real]
Sets the amount of diffusion equation-style smoothing that will be applied to the potential
energy surface when using the SMOOTH force field. The real number option is equivalent to
the “time” value in the original Piela, et al. formalism; the larger the value, the greater the
smoothing. The default value is zero, meaning that no smoothing will be applied.
DEGREES-FREEDOM [integer]
Sets the number of degrees of freedom during a dynamics calculation. The integer modifier
is used by thermostating methods and in other places as the number of degrees of freedom,
overriding the value determined by the Tinker code at dynamics startup. In the absence of the
keyword, the programs will automatically compute the correct value based on the number
of atoms active during dynamics, bond or other constraints, and use of periodic boundary
conditions.
DELCX-EPS [real]
Sets the value of the epsilon tolerance value to be used in the Delauney triangulation portion
of the AlphaMol surface area and volume calculations. In the absence of the DELCX-EPS
keyword, a default value of 0.0000000001 is used.
DELTA-HALGREN [real]

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Sets the value of the delta parameter in Halgren’s buffered 14-7 vdw potential energy func-
tional form. In the absence of the DELTA-HALGREN keyword, a default value of 0.07 is used.
DESCREEN-HYDROGEN
DESCREEN-OFFSET
DEWALD
Turns on the use of smooth particle mesh Ewald (PME) summation during computation of dis-
persion interactions in periodic systems. By default, in the absence of the DEWALD keyword,
distance-based cutoffs are used for dispersion interactions.
DEWALD-ALPHA [real]
Sets the value of the Ewald coefficient which controls the width of the Gaussian screen-
ing charges during particle mesh Ewald summation for dispersion. In the absence of the
DEWALD-ALPHA keyword, the EWALD-ALPHA is used, or a value is chosen which causes
interactions outside the real-space cutoff to be below a fixed tolerance. For most standard
applications of dispersion Ewald summation, the program default should be used.
DEWALD-CUTOFF [real]
Sets the value in Angstroms of the real-space distance cutoff for use during Ewald summation
for dispersion interactions. By default, in the absence of the DEWALD-CUTOFF keyword, a
value of 7.0 is used.
DIELECTRIC [real]
Sets the value of the bulk dielectric constant used to damp all electrostatic interaction en-
ergies for any of the Tinker electrostatic potential functions. The default value is force field
dependent, but is usually equal to 1.0 (for Allinger’s MM force fields the default is 1.5).
DIELECTRIC-OFFSET [real]
Sets the value in Angstroms of the dielectric offset constant by which solvation atomic radii
are reduced during computation of Born radii. By default, in the absence of the DIELECTRIC-
OFFSET keyword, a value of 0.09 is used.
DIFFUSE-CHARGE [real]
Used during potential function smoothing procedures to specify the effective diffusion coeffi-
cient applied to the smoothed form of the Coulomb’s Law charge-charge potential function.
In the absence of the DIFFUSE-CHARGE keyword, a default value of 3.5 is used.
DIFFUSE-TORSION [real]
Used during potential function smoothing procedures to specify the effective diffusion coeffi-
cient applied to the smoothed form of the torsion angle potential function. In the absence of
the DIFFUSE-TORSION keyword, a default value of 0.0225 is used.
DIFFUSE-VDW [real]
Used during potential function smoothing procedures to specify the effective diffusion coef-
ficient applied to the smoothed Gaussian approximation to the Lennard-Jones van der Waals
potential function. In the absence of the DIFFUSE-VDW keyword, a default value of 1.0 is
used.
DIGITS [integer]
Controls the number of digits of precision output by Tinker in reporting potential energies
and atomic coordinates. The allowed values for the integer modifier are 4, 6 and 8. Input

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values less than 4 will be set to 4, and those greater than 8 will be set to 8. Final energy
values reported by most Tinker programs will contain the specified number of digits to the
right of the decimal point. The number of decimal places to be output for atomic coordinates
is generally two larger than the value of DIGITS. In the absence of the DIGITS keyword a
default value of 4 is used, and energies will be reported to 4 decimal places with coordinates
to 6 decimal places.
DIPOLE [2 integers & 2 reals]
Provides the values for a single bond dipole electrostatic parameter. The integer modifiers
give the atom type numbers for the two kinds of atoms involved in the bond dipole which is
to be defined. The real number modifiers give the value of the bond dipole in Debyes and
the position of the dipole site along the bond. If the bond dipole value is positive, then the
first of the two atom types is the positive end of the dipole. For a negative bond dipole value,
the first atom type listed is negative. The position along the bond is an optional modifier that
gives the postion of the dipole site as a fraction between the first atom type (position=0) and
the second atom type (position=1). The default for the dipole position in the absence of a
specified value is 0.5, placing the dipole at the midpoint of the bond.
DIPOLE-CUTOFF [real]
Sets the cutoff distance value in Angstroms for bond dipole-bond dipole electrostatic potential
energy interactions. The energy for any pair of bond dipole sites beyond the cutoff distance
will be set to zero. Other keywords can be used to select a smoothing scheme near the cutoff
distance. The default cutoff distance in the absence of the DPL-CUTOFF keyword is essentially
infinite for nonperiodic systems and 10.0 for periodic systems.
DIPOLE-TAPER [real]
Modifies the cutoff windows for bond dipole-bond dipole electrostatic potential energy inter-
actions. It is similar in form and action to the TAPER keyword, except that its value applies
only to the vdw potential. The default value in the absence of the DPL-TAPER keyword is to
begin the cutoff window at 0.75 of the dipole cutoff distance.
DIPOLE3 [2 integers & 2 reals]
Provides the values for a single bond dipole electrostatic parameter specific to atoms in 3-
membered rings. The integer modifiers give the atom type numbers for the two kinds of
atoms involved in the bond dipole which is to be defined. The real number modifiers give the
value of the bond dipole in Debyes and the position of the dipole site along the bond. The
default for the dipole position in the absence of a specified value is 0.5, placing the dipole at
the midpoint of the bond. If any DIPOLE3 keywords are present, either in the master force
field parameter file or the keyfile, then Tinker requires that special DIPOLE3 parameters be
given for all bond dipoles in 3-membered rings. In the absence of any DIPOLE3 keywords,
standard DIPOLE parameters will be used for bonds in 3-membered rings.
DIPOLE4 [2 integers & 2 reals]
Provides the values for a single bond dipole electrostatic parameter specific to atoms in 4-
membered rings. The integer modifiers give the atom type numbers for the two kinds of
atoms involved in the bond dipole which is to be defined. The real number modifiers give the
value of the bond dipole in Debyes and the position of the dipole site along the bond. The
default for the dipole position in the absence of a specified value is 0.5, placing the dipole at
the midpoint of the bond. If any DIPOLE4 keywords are present, either in the master force
field parameter file or the keyfile, then Tinker requires that special DIPOLE4 parameters be

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given for all bond dipoles in 4-membered rings. In the absence of any DIPOLE4 keywords,
standard DIPOLE parameters will be used for bonds in 4-membered rings.
DIPOLE5 [2 integers & 2 reals]
Provides the values for a single bond dipole electrostatic parameter specific to atoms in 5-
membered rings. The integer modifiers give the atom type numbers for the two kinds of
atoms involved in the bond dipole which is to be defined. The real number modifiers give the
value of the bond dipole in Debyes and the position of the dipole site along the bond. The
default for the dipole position in the absence of a specified value is 0.5, placing the dipole at
the midpoint of the bond. If any DIPOLE5 keywords are present, either in the master force
field parameter file or the keyfile, then Tinker requires that special DIPOLE5 parameters be
given for all bond dipoles in 5-membered rings. In the absence of any DIPOLE5 keywords,
standard DIPOLE parameters will be used for bonds in 5-membered rings.
DIPOLETERM [NONE / ONLY]
Controls use of the dipole-dipole potential energy term between pairs of bond dipoles. In the
absence of a modifying option, this keyword turns on use of the potential. The NONE option
turns off use of this potential energy term. The ONLY option turns off all potential energy
terms except for this one.
DIRECT-11-SCALE [real]
Provides a multiplicative scale factor that is applied to the permanent (direct) field due to
atoms within a polarization group during an induced dipole calculation, i.e., atoms that are
in the same polarization group as the atom being polarized. The default value of 0.0 is used,
if the DIRECT-11-SCALE keyword is not given in either the parameter file or the keyfile.
DIRECT-12-SCALE [real]
Provides a multiplicative scale factor that is applied to the permanent (direct) field due to
atoms in 1-2 polarization groups during an induced dipole calculation, i.e., atoms that are
in polarization groups directly connected to the group containing the atom being polarized.
The default value of 0.0 is used, if the DIRECT-12-SCALE keyword is not given in either the
parameter file or the keyfile.
DIRECT-13-SCALE [real]
Provides a multiplicative scale factor that is applied to the permanent (direct) field due to
atoms in 1-3 polarization groups during an induced dipole calculation, i.e., atoms that are
in polarization groups separated by one group from the group containing the atom being
polarized. The default value of 0.0 is used, if the DIRECT-13-SCALE keyword is not given in
either the parameter file or the keyfile.
DIRECT-14-SCALE [real]
Provides a multiplicative scale factor that is applied to the permanent (direct) field due to
atoms in 1-4 polarization groups during an induced dipole calculation, i.e., atoms that are
in polarization groups separated by two groups from the group containing the atom being
polarized. The default value of 1.0 is used, if the DIRECT-14-SCALE keyword is not given in
either the parameter file or the keyfile.
DISP-12-SCALE [real]
Provides a multiplicative scale factor that is applied to dispersion potential interactions be-
tween 1-2 connected atoms, i.e., atoms that are directly bonded. The default value of 0.0 is
used, if the DISP-12-SCALE keyword is not given in either the parameter file or the keyfile.

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DISP-13-SCALE [real]
Provides a multiplicative scale factor that is applied to dispersion potential interactions be-
tween 1-3 connected atoms, i.e., atoms separated by two covalent bonds. The default value
of 0.0 is used, if the DISP-13-SCALE keyword is not given in either the parameter file or the
keyfile.
DISP-14-SCALE [real]
Provides a multiplicative scale factor that is applied to dispersion potential interactions be-
tween 1-4 connected atoms, i.e., atoms separated by three covalent bonds. The default value
of 1.0 is used, if the DISP-14-SCALE keyword is not given in either the parameter file or the
keyfile.
DISP-15-SCALE [real]
Provides a multiplicative scale factor that is applied to dispersion potential interactions be-
tween 1-5 connected atoms, i.e., atoms separated by four covalent bonds. The default value
of 1.0 is used, if the DISP-15-SCALE keyword is not given in either the parameter file or the
keyfile.
DISP-CORRECTION
Turns on the use of an isotropic long-range correction term to approximately account for
dispersion interactions beyond the cutoff distance. This correction modifies the value of the
dispersion energy and virial due to dispersion interactions, but has no effect on the gradient
of the dispersion energy.
DISP-CUTOFF [real]
Sets the cutoff distance value in Angstroms for dispersion potential energy interactions. The
energy for any pair of sites beyond the cutoff distance will be set to zero. Other keywords can
be used to select a smoothing scheme near the cutoff distance. The default cutoff distance
in the absence of the DISP-CUTOFF keyword is infinite for nonperiodic systems and 9.0 for
periodic systems.
DISP-LIST
Turns on the use of pairwise neighbor lists for dispersion interactions. This method will yield
identical energetic results to the standard double loop method.
DISP-TAPER [real]
Modifies the cutoff window for dispersion potential energy interactions. It is similar in form
and action to the TAPER keyword, except that its value applies only to the dispersion po-
tential. The default value in the absence of the DISP-TAPER keyword is to begin the cutoff
window at 0.9 of the corresponding cutoff distance.
DISPERSION [1 integer, 2 reals]
Provides values for a single dispersion parameter. The integer modifier, if positive, gives the
atom class number for which the dispersion parameters are to be defined. If the integer
modifier is negative, then the parameter values to follow apply only to the individual atom
whose atom number is the negative of the modifier. The real number modifiers give the root
sixth-power “C6” coefficient for the atom class and the “alpha” exponent used in damping the
dispersion interaction.
DISPERSIONTERM [NONE / ONLY]
Controls use of the pairwise dispersion potential energy term between pairs of atoms. In the
absence of a modifying option, this keyword turns on use of the potential. The NONE option

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turns off use of this potential energy term. The ONLY option turns off all potential energy
terms except for this one.
DIVERGE [real]
Used by the SADDLE program to set the maximum allowed value of the ratio of the gradi-
ent length along the path to the total gradient norm at the end of a cycle of minimization
perpendicular to the path. If the value provided by the DIVERGE keyword is exceeded, then
another cycle of maximization along the path is required. A default value of 0.005 is used in
the absence of the DIVERGE keyword.
DODECAHEDRON
Specifies that the periodic “box” is a rhombic dodecahedron with maximal distance between
parallel faces across the periodic box as given by the A-AXIS keyword. The box is oriented
such that the b-axis is set equal to the a-axis, and the c-axis is longer by a factor of the
square root of 2. The volume of the resulting rhombic dodecahedron is half the volume of the
corresponding rectangular prism. All other unit cell and size-defining keywords are ignored
if the DODECAHEDRON keyword is present.
DPME-GRID [3 integers]
Sets the dimensions of the reciprocal space grid used during particle mesh Ewald summation
for dispersion. The three modifiers give the size along the X-, Y- and Z-axes, respectively. If
either the Y- or Z-axis dimensions are omitted, then they are set equal to the X-axis dimension.
The default in the absence of the PME-GRID keyword is to set the grid size along each axis to
the smallest power of 2, 3 and/or 5 which is at least as large as 0.8 times the axis length in
Angstoms.
DPME-ORDER [integer]
Sets the order of the B-spline interpolation used during particle mesh Ewald summation for
dispersion. A default value of 4 is used in the absence of the DPME-ORDER keyword.
ECHO [text string]
Causes whatever text follows it on the keyword line to be copied directly to the output file.
This keyword is also active in parameter files. It has no default value; if no text follows the
ECHO keyword, a blank line is placed in the output file.
ELE-LAMBDA
Sets the value of the lambda scaling parameters for electrostatic interactions during free
energy calculations and similar. The real number modifier sets the position along path from
the initial state (lambda=0) to the final state (lambda=1). Alternatively, this parameter can
set the state of decoupling or annihilation for specified groups from none (lambda=1) to
complete (lambda=0). The groups involved in the scaling are given separately via LIGAND
or MUTATE keywords.
ELECTNEG [3 integers & 1 real]
Provides the values for a single electronegativity bond length correction parameter. The first
two integer modifiers give the atom class numbers of the atoms involved in the bond to be
corrected. The third integer modifier is the atom class of an electronegative atom. In the case
of a primary correction, an atom of this third class must be directly bonded to an atom of the
second atom class. For a secondary correction, the third class is one atom removed from an
atom of the second class. The real number modifier is the value in Angstroms by which the
original ideal bond length is to be corrected.

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ELECTRIC [real]
Specifies a value for the so-called “electric constant” allowing conversion unit of electrostatic
potential energy values from electrons^2/Angstrom to kcal/mol. Internally, Tinker stores
a default value for this constant as 332.063713 based on CODATA reference values. Since
different force fields are intended for use with slightly different values, this keyword allows
overriding the default value.
ENFORCE-CHIRALITY
Causes the chirality found at chiral tetravalent centers in the input structure to be maintained
during Tinker calculations. The test for chirality is not exhaustive; two identical monova-
lent atoms connected to a center cause it to be marked as non-chiral, but large equivalent
substituents are not detected. Trivalent “chiral” centers, for example the alpha carbon in
united-atom protein structures, are not enforced as chiral.
EPSILONRULE [GEOMETRIC / ARITHMETIC / HARMONIC / HHG / W-H]
Selects the combining rule used to derive the epsilon value for van der Waals interactions.
The default in the absence of the EPSILONRULE keyword is to use the GEOMETRIC mean of
the individual epsilon values of the two atoms involved in the van der Waals interaction.
EWALD
Turns on the use of smooth particle mesh Ewald (PME) summation during computation of
partial charge, atomic multipole and polarization interactions in periodic systems. By de-
fault, in the absence of the EWALD keyword, distance-based cutoffs are used for electrostatic
interactions.
EWALD-ALPHA [real]
Sets the value of the Ewald coefficient which controls the width of the Gaussian screening
charges during particle mesh Ewald summation for multipole electrostatics, and by default
for other PME interactions. In the absence of the EWALD-ALPHA keyword, a value is chosen
which causes interactions outside the real-space cutoff to be below a fixed tolerance. For most
standard applications of Ewald summation, the program default should be used.
EWALD-BOUNDARY
Invokes the use of insulating (ie, vacuum) boundary conditions during Ewald summation,
corresponding to the media surrounding the system having a dielectric value of 1. The default
in the absence of the EWALD-BOUNDARY keyword is to use conducting (ie, tinfoil) boundary
conditions where the surrounding media is assumed to have an infinite dielectric value.
EWALD-CUTOFF [real]
Sets the value in Angstroms of the real-space distance cutoff for use during Ewald summation.
By default, in the absence of the EWALD-CUTOFF keyword, a value of 7.0 is used.
EXCHANGE-POLAR [S2U / S2 / G]
Selects the type of overlap function to be used in the short-range damping of atomic polariz-
abilities to account for exchange-polarization. Options include two methods based on over-
lap, S, and a Gaussian approximation. The default in the absence of the EXCHANGE-POLAR
keyword is to use the unified square of the overlap, S2U.
EXTERNAL-FIELD [3 reals]
Selects the value in megavolts per centimeter (MV/cm) of external electric field components
to apply uniformly to the system. The three real modifiers specify the X-, Y- and Z-components

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Tinker User's Guide

of the applied electric field vector. The default in the absence of the EXTERNAL-FIELD key-
word is to not use an external field.
EXCHPOL [integer, 3 reals, integer]
Provides the values for the variable polarizability model for treating exchange polarization.
The first integer modifier is the atom class number for the which parameters are defined. The
three real modifiers provide the spring force constant, an atomic size value and a damping co-
efficient. The final integer modifier is 1 if this atom class actively uses exchange polarization,
and 0 this class is only passively used in exchange polarization.
EXIT-PAUSE
Causes Tinker programs to pause and wait for a carriage return at the end of executation prior
to returning control to the operating system. This is useful to keep the execution window
open following termination on machines running Microsoft Windows or Apple macOS. The
default in the absence of the EXIT-PAUSE keyword, is to return control to the operating system
immediately at program termination.
EXTRATERM [NONE / ONLY]
Controls use of the user defined extra potential energy term. In the absence of a modifying
option, this keyword turns on use of the potential. The NONE option turns off use of this
potential energy term. The ONLY option turns off all potential energy terms except for this
one.
FCTMIN [real]
Sets a convergence criterion for successful completion of an optimization. If the value of
the optimization objective function, typically the potential energy, falls below the value set
by FCTMIN, then the optimization is deemed to have converged. The default value in the
absence of the FCTMIN keyword is -1000000, effectively removing this criterion as a possible
agent for termination.
FFT-PACKAGE [FFTPACK / FFTW]
Specifies the fast Fourier transform package to be used in reciprocal space calculations as part
of particle mesh Ewald summation. The default in the absence of the FFT-PACKAGE keyword
is to use FFTPACK for serial, single-threaded calculations, and FFTW for OpenMP parallel
calculations using multiple threads.
FIT-ANGLE
FIT-BOND
FIT-OPBEND
FIT-STRBND
FIT-TORSION
FIT-UREY
FIX-ANGLE
FIX-ATOM-DIPOLE
FIX-BOND

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FIX-CHGPEN
Causes the individual charge penetration alpha parameters to be held fixed at their input
values during the fitting of an electrostatic model to target values of the electrostatic potential
on a grid of points surrounding an input system of interest. In the absence of the FIX-CHGPEN
keyword, alpha values are allowed to vary during the fitting procedure for models using
charge penetration.
FIX-DIPOLE
Causes the individual dipole components of atomic multipole parameters to be held fixed at
their input values during the fitting of an electrostatic model to target values of the electro-
static potential on a grid of points surrounding an input system of interest. In the absence of
the FIX-DIPOLE keyword, dipole values are allowed to vary during the fitting procedure.
FIX-MONOPOLE
Causes the individual monopole components of atomic multipole parameters to be held fixed
at their input values during the fitting of an electrostatic model to target values of the elec-
trostatic potential on a grid of points surrounding an input system of interest. In the absence
of the FIX-MULTIPOLE keyword, monopole values are allowed to vary during the fitting pro-
cedure.
FIX-OPBEND
FIX-QUADRUPOLE
Causes the individual quadrupole components of atomic multipole parameters to be held
fixed at their input values during the fitting of an electrostatic model to target values of the
electrostatic potential on a grid of points surrounding an input system of interest. In the
absence of the FIX-QUADRUPOLE keyword, quadrupole values are allowed to vary during
the fitting procedure.
FIX-STRBND
FIX-TORSION
FIX-UREY
FORCEFIELD [name]
Provides a name for the force field to be used in the current calculation. Its value is usually set
in the master force field parameter file for the calculation (see the PARAMETERS keyword)
instead of in the keyfile.
FRICTION [real]
Sets the value of the frictional coefficient in 1/ps for use with stochastic dynamics. The default
value used in the absence of the FRICTION keyword is 91.0, which is generally appropriate
for water.
FRICTION-SCALING
Turns on the use of atomic surface area-based scaling of the frictional coefficient during
stochastic dynamics. When in use, the coefficient for each atom is multiplied by that atom’s
fraction of exposed surface area. The default in the absence of the keyword is to omit the
scaling and use the full coefficient value for each atom.
GAMMA [real]
Sets the value of the gamma angle of a crystal unit cell, i.e., the angle between the a-axis and

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b-axis of a unit cell, or, equivalently, the angle between the X-axis and Y-axis of a periodic box.
The default value in the absence of the GAMMA keyword is to set the gamma angle equal to
the gamma angle as given by the keyword ALPHA.
GAMMA-HALGREN [real]
Sets the value of the gamma parameter in Halgren’s buffered 14-7 vdw potential energy
functional form. In the absence of the GAMMA-HALGREN keyword, a default value of 0.12
is used.
GAMMAMIN [real]
Sets the convergence target value for gamma during searches for maxima along the quadratic
synchronous transit used by the SADDLE program. The value of gamma is the square of
the ratio of the gradient projection along the path to the total gradient. A default value of
0.00001 is used in the absence of the GAMMAMIN keyword.
GAUSSTYPE [LJ-2 / LJ-4 / MM2-2 / MM3-2 / IN-PLACE]
Specifies the underlying vdw form that a Gaussian vdw approximation will attempt to fit
as the number of terms to be used in a Gaussian approximation of the Lennard-Jones van
der Waals potential. The text modifier gives the name of the functional form to be used.
Thus LJ-2 as a modifier will result in a 2-Gaussian fit to a Lennard-Jones vdw potential. The
GAUSSTYPE keyword only takes effect when VDWTYPE is set to GAUSSIAN. This keyword
has no default value.
GK-RADIUS
GKC
GKR
GROUP [integer, integer list]
Defines an atom group as a substructure within the full input molecular structure. The value
of the first integer is the group number which must be in the range from 1 to the maximum
number of allowed groups. The remaining intergers give the atom or atoms contained in this
group as one or more atom numbers or ranges. Multiple keyword lines can be used to specify
additional atoms in the same group. Note that an atom can only be in one group, the last
group to which it is assigned is the one used.
GROUP-INTER
Assigns a value of 1.0 to all inter-group interactions and a value of 0.0 to all intra-group
interactions. For example, combination with the GROUP-MOLECULE keyword provides for
rigid-body calculations.
GROUP-INTRA
Assigns a value of 1.0 to all intra-group interactions and a value of 0.0 to all inter-group
interactions.
GROUP-MOLECULE
Sets each individual molecule in the system to be a separate atom group, but does not assign
weights to group-group interactions.
GROUP-SELECT [2 integers, real]
Assigns a weight in the final potential energy of a specified set of intra- or intergroup inter-
actions. The integer modifiers give the group numbers of the groups involved. If the two

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numbers are the same, then an intragroup set of interactions is specified. The real modifier
gives the weight by which all energetic interactions in this set will be multiplied before incor-
poration into the final potential energy. If omitted as a keyword modifier, the weight will be
set to 1.0 by default. If any SELECT-GROUP keywords are present, then any set of interac-
tions not specified in a SELECT-GROUP keyword is given a zero weight. The default when no
SELECT-GROUP keywords are specified is to use all intergroup interactions with a weight of
1.0 and to set all intragroup interactions to zero.
HBOND [2 integers & 2 reals]
Provides the values for the MM3-style directional hydrogen bonding parameters for a single
pair of atoms. The integer modifiers give the pair of atom class numbers for which hydrogen
bonding parameters are to be defined. The two real number modifiers give the values of the
minimum energy contact distance in Angstroms and the well depth at the minimum distance
in kcal/mole.
HCT-ELEMENT
HCT-SCALE
HEAVY-HYDROGEN [real]
Turns on use of hydrogen mass repartitioning (HMR) and sets the target value for hydrogen
masses. HMR transfers atomic mass from heavy atoms to their attached hydrogen atoms.
Mass transfer is allowed until the hydrogen mass target is reached, or until a heavy atom and
its attached hydrogens all have equal mass. A default value of 4.0 is used as the hydrogen
mass target in the absence of the HEAVY-HYDROGEN keyword.
HESSIAN-CUTOFF [real]
Defines a lower limit for significant Hessian matrix elements. During computation of the
Hessian matrix of partial second derivatives, any matrix elements with absolute value below
HESS-CUTOFF will be set to zero and omitted from the sparse matrix Hessian storage scheme
used by Tinker. For most calculations, the default in the absence of this keyword is zero, i.e.,
all elements will be stored. For most truncated Newton optimizations the Hessian cutoff will
be chosen dynamically by the optimizer.
HGUESS [real]
Sets an initial guess for the average value of the diagonal elements of the scaled inverse
Hessian matrix used by the optimally conditioned variable metric optimization routine. A
default value of 0.4 is used in the absence of the HGUESS keyword.
IEL-SCF
IMPROPER [4 integers & 2 reals]
Provides the values for a single CHARMM-style improper dihedral angle parameter. The inte-
ger modifiers give the atom class numbers for the four kinds of atoms involved in the torsion
which is to be defined. The real number modifiers give the force constant value for the devi-
ation from the target improper torsional angle, and the target value for the torsional angle,
respectively. The default units for the improper force constant are kcal/mole/radian^2, but
this can be controlled via the IMPROPUNIT keyword.
IMPROPTERM [NONE / ONLY]
Controls use of the CHARMM-style improper dihedral angle potential energy term. In the
absence of a modifying option, this keyword turns on use of the potential. The NONE option

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turns off use of this potential energy term. The ONLY option turns off all potential energy
terms except for this one.
IMPROPUNIT [real]
Sets the scale factor needed to convert the energy value computed by the CHARMM-style
improper dihedral angle potential into units of kcal/mole. The correct value is force field
dependent and typically provided in the header of the master force field parameter file. The
default value of (180/Pi)^2 = 0.0003046 is used, if the IMPROPUNIT keyword is not given
in the force field parameter file or the keyfile.
IMPTORS [4 integers & up to 3 real/real/integer triples]
Provides the values for a single AMBER-style improper torsional angle parameter. The first
four integer modifiers give the atom class numbers for the atoms involved in the improper
torsional angle to be defined. By convention, the third atom class of the four is the trigonal
atom on which the improper torsion is centered. The torsional angle computed is literally that
defined by the four atom classes in the order specified by the keyword. Each of the remaining
triples of real/real/integer modifiers give the half-amplitude, phase offset in degrees and
periodicity of a particular improper torsional term, respectively. Periodicities through 3-fold
are allowed for improper torsional parameters.
IMPTORSTERM [NONE / ONLY]
Controls use of the AMBER-style improper torsional angle potential energy term. In the
absence of a modifying option, this keyword turns on use of the potential. The NONE option
turns off use of this potential energy term. The ONLY option turns off all potential energy
terms except for this one.
IMPTORSUNIT [real]
Sets the scale factor needed to convert the energy value computed by the AMBER-style im-
proper torsional angle potential into units of kcal/mole. The correct value is force field depen-
dent and typically provided in the header of the master force field parameter file. The default
value of 1.0 is used, if the IMPTORSUNIT keyword is not given in the force field parameter
file or the keyfile.
INACTIVE [integer list]
Sets the list of inactive atoms during a Tinker computation. Individual potential energy terms
are not computed when all atoms involved in the term are inactive. For Cartesian space cal-
culations, inactive atoms are not allowed to move. For torsional space calculations, rotations
are not allowed when there are inactive atoms on both sides of the rotated bond. Multiple
INACTIVE lines can be present in the keyfile, and on each line the keyword can be followed
by one or more atom numbers or ranges. If any INACTIVE keys are found, all atoms are
set to active except those listed on the INACTIVE lines. The ACTIVE keyword overrides all
INACTIVE keywords found in the keyfile.
INDUCE-12-SCALE [real]
Provides a multiplicative scale factor that is applied to the induced (mutual) field between 1-2
connected atoms during an induced dipole calculation involving charge penetration damping,
i.e., atoms that are directly bonded. The default value of 1.0 is used, if the INDUCE-12-SCALE
keyword is not given in either the parameter file or the keyfile.
INDUCE-13-SCALE [real]
Provides a multiplicative scale factor that is applied to the induced (mutual) field between 1-3

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connected atoms during an induced dipole calculation involving charge penetration damping,
i.e., atoms separated by two covalent bonds. The default value of 1.0 is used, if the INDUCE-
13-SCALE keyword is not given in either the parameter file or the keyfile.
INDUCE-14-SCALE [real]
Provides a multiplicative scale factor that is applied to the induced (mutual) field between 1-4
connected atoms during an induced dipole calculation involving charge penetration damping,
i.e., atoms separated by three covalent bonds. The default value of 1.0 is used, if the INDUCE-
14-SCALE keyword is not given in either the parameter file or the keyfile.
INDUCE-15-SCALE [real]
Provides a multiplicative scale factor that is applied to the induced (mutual) field between 1-5
connected atoms during an induced dipole calculation involving charge penetration damping,
i.e., atoms separated by four covalent bonds. The default value of 1.0 is used, if the INDUCE-
15-SCALE keyword is not given in either the parameter file or the keyfile.
INTEGRATOR [VERLET / BEEMAN / RESPA / BAOAB / NOSE-HOOVER / BUSSI / GHMC /
STOCHASTIC / RIGIDBODY]
Chooses the integration method for propagation of dynamics trajectories. The keyword is
followed on the same line by the name of the option. The VERLET modifier specifies the Ve-
locity Verlet method. BEEMAN is the velocity form of Bernie Brook’s “Better Beeman” method.
RESPA is a two-stage multiple time step integrator that splits bonded and nonbonded interac-
tions. Both NOSE-HOOVER and BUSSI select integrators coupled to a thermostat and baro-
stat of the same name. STOCHASTIC is a Velocity Verlet-based stochastic dynamics method.
RIGIDBODY is an Euler angle-based rigid-body dynamics method. The default integration
scheme for molecular dynamics is to use the BEEMAN method.
INTMAX [integer]
Sets the maximum number of interpolation cycles that will be allowed during the line search
phase of an optimization. All gradient-based Tinker optimization routines use a common
line search routine involving quadratic extrapolation and cubic interpolation. If the value
of INTMAX is reached, an error status is set for the line search and the search is repeated
with a much smaller initial step size. The default value in the absence of this keyword is
optimization routine dependent, but is usually in the range 5 to 10.
LAMBDA [real]
Sets the value of the lambda scaling parameters for electrostatic, vdw and torsional interac-
tions during free energy calculations and similar. The real number modifier sets the position
along path from the initial state (lambda=0) to the final state (lambda=1). Alternatively,
this parameter can set the state of decoupling or annihilation for specified groups from none
(lambda=1) to complete (lambda=0). The groups involved in the scaling are given sepa-
rately via LIGAND or MUTATE keywords.
LBFGS-VECTORS [integer]
Sets the number of correction vectors used by the limited-memory L-BFGS optimization rou-
tine. The current maximum allowable value, and the default in the absence of the LBFGS-
VECTORS keyword is 15.
LIGAND
LIGHTS
Turns on Method of Lights neighbor generation for the partial charge electrostatics and any of

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the van der Waals potentials. This method will yield identical energetic results to the standard
double loop method. Method of Lights will be faster when the volume of a sphere with radius
equal to the nonbond cutoff distance is significantly less than half the volume of the total
system (i.e., the full molecular system, the crystal unit cell or the periodic box). It requires
less storage than pairwise neighbor lists.
LIST-BUFFER [real]
Sets the size of the neighbor list buffer in Angstroms for potential energy functions. This value
is added to the actual cutoff distance to determine which pairs will be kept on the neighbor
list. This buffer value is used for all potential function neighbor lists. The default value in the
absence of the LIST-BUFFER keyword is 2.0 Angstroms.
MAXITER [integer]
Sets the maximum number of minimization iterations that will be allowed for any Tinker pro-
gram that uses any of the nonlinear optimization routines. The default value in the absence
of this keyword is program dependent, but is always set to a very large number.
METAL [integer]
Provides the values for a single transition metal ligand field parameter. Note the current
version just reads an atom class number and does not set any parameters. This keyword is
present in the code, but not active in the current version of Tinker.
METALTERM [NONE / ONLY]
Controls use of the transition metal ligand field potential energy term. In the absence of a
modifying option, this keyword turns on use of the potential. The NONE option turns off use
of this potential energy term. The ONLY option turns off all potential energy terms except for
this one.
MMFF-PIBOND
MMFFANGLE
MMFFAROM
MMFFBCI
MMFFBOND
MMFFBONDER
MMFFCOVRAD
MMFFDEFSTBN
MMFFEQUIV
MMFFOPBEND
MMFFPBCI
MMFFPROP
MMFFSTRBND
MMFFTORSION
MMFFVDW

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MPOLE-12-SCALE [real]
Provides a multiplicative scale factor that is applied to permanent atomic multipole electro-
static interactions between 1-2 connected atoms, i.e., atoms that are directly bonded. The
default value of 0.0 is used, if the MPOLE-12-SCALE keyword is not given in either the pa-
rameter file or the keyfile.
MPOLE-13-SCALE [real]
Provides a multiplicative scale factor that is applied to permanent atomic multipole electro-
static interactions between 1-3 connected atoms, i.e., atoms separated by two covalent bonds.
The default value of 0.0 is used, if the MPOLE-13-SCALE keyword is not given in either the
parameter file or the keyfile.
MPOLE-14-SCALE [real]
Provides a multiplicative scale factor that is applied to permanent atomic multipole elec-
trostatic interactions between 1-4 connected atoms, i.e., atoms separated by three covalent
bonds. The default value of 1.0 is used, if the MPOLE-14-SCALE keyword is not given in
either the parameter file or the keyfile.
MPOLE-15-SCALE [real]
Provides a multiplicative scale factor that is applied to permanent atomic multipole electro-
static interactions between 1-5 connected atoms, i.e., atoms separated by four covalent bonds.
The default value of 1.0 is used, if the MPOLE-15-SCALE keyword is not given in either the
parameter file or the keyfile.
MPOLE-CUTOFF [real]
Sets the cutoff distance value in Angstroms for atomic multipole potential energy interactions.
The energy for any pair of sites beyond the cutoff distance will be set to zero. Other keywords
can be used to select a smoothing scheme near the cutoff distance. The default cutoff distance
in the absence of the MPOLE-CUTOFF keyword is infinite for nonperiodic systems and 9.0 for
periodic systems.
MPOLE-LIST
Turns on pairwise neighbor lists for atomic multipole electrostatics and induced dipole po-
larization. This method will yield identical energetic results to the standard double loop
methods.
MPOLE-TAPER [real]
Modifies the cutoff window for atomic multipole potential energy interactions. It is similar
in form and action to the TAPER keyword, except that its value applies only to the atomic
multipole potential. The default value in the absence of the MPOLE-TAPER keyword is to
begin the cutoff window at 0.65 of the corresponding cutoff distance.
MULTIPOLE [5 lines with: 3 or 4 integers & 1 real; 3 reals; 1 real; 2 reals; 3 reals]
Provides the values for a set of atomic multipole parameters at a single site. A complete
keyword entry consists of three consequtive lines, the first line containing the MULTIPOLE
keyword and the two following lines. The first line contains three integers which define the
atom type on which the multipoles are centered, and the Z-axis and X-axis defining atom
types for this center. The optional fourth integer contains the Y-axis defining atom type, and
is only required for locally chiral multipole sites. The real number on the first line gives the
monopole (atomic charge) in electrons. The second line contains three real numbers which
give the X-, Y- and Z-components of the atomic dipole in electron-Ang. The final three lines,

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consisting of one, two and three real numbers give the upper triangle of the traceless atomic
quadrupole tensor in electron-Ang^2.
MULTIPOLETERM [NONE / ONLY]
Controls use of the atomic multipole electrostatics potential energy term. In the absence of a
modifying option, this keyword turns on use of the potential. The NONE option turns off use
of this potential energy term. The ONLY option turns off all potential energy terms except for
this one.
MUTATE [3 integers]
Specifies atoms to be mutated during free energy perturbation calculations. The first integer
modifier gives the atom number of an atom in the current system. The final two modifier
values give the atom types corresponding the the lambda=0 and lambda=1 states of the
specified atom.
MUTUAL-11-SCALE [real]
Provides a multiplicative scale factor that is applied to the induced (mutual) field due to atoms
within a polarization group during an induced dipole calculation involving Thole damping,
i.e., atoms that are in the same polarization group as the atom being polarized. The default
value of 1.0 is used, if the MUTUAL-11-SCALE keyword is not given in either the parameter
file or the keyfile.
MUTUAL-12-SCALE [real]
Provides a multiplicative scale factor that is applied to the induced (mutual) field due to atoms
in 1-2 polarization groups during an induced dipole calculation involving Thole damping, i.e.,
atoms that are in polarization groups directly connected to the group containing the atom
being polarized. The default value of 1.0 is used, if the MUTUAL-12-SCALE keyword is not
given in either the parameter file or the keyfile.
MUTUAL-13-SCALE [real]
Provides a multiplicative scale factor that is applied to the induced (mutual) field due to atoms
in 1-3 polarization groups during an induced dipole calculation involving Thole damping, i.e.,
atoms that are in polarization groups separated by one group from the group containing the
atom being polarized. The default value of 1.0 is used, if the MUTUAL-13-SCALE keyword is
not given in either the parameter file or the keyfile.
MUTUAL-14-SCALE [real]
Provides a multiplicative scale factor that is applied to the induced (mutual) field due to atoms
in 1-4 polarization groups during an induced dipole calculation involving Thole damping, i.e.,
atoms that are in polarization groups separated by two groups from the group containing the
atom being polarized. The default value of 1.0 is used, if the MUTUAL-14-SCALE keyword is
not given in either the parameter file or the keyfile.
NECK-CORRECTION
NEIGHBOR-GROUPS
Causes the attached atom to be used in determining the charge-charge neighbor distance for
all monovalent atoms in the molecular system. Its use causes all monovalent atoms to be
treated the same as their attached atoms for purposes of including or scaling 1-2, 1-3 and 1-4
interactions. This option works only for the simple charge-charge electrostatic potential; it
does not affect bond dipole or atomic multipole potentials. The NEIGHBOR-GROUPS scheme
is similar to that used by ENCAD and other force fields.

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NEIGHBOR-LIST
Turns on pairwise neighbor lists for partial charge electrostatics, atomic multipole electrostat-
ics, induced dipole polarization and any of the van der Waals potentials. This method will
yield identical energetic results to the standard double loop method.
NEUTRAL-GROUPS
Causes the attached atom to be used in determining the charge-charge interaction cutoff dis-
tance for all monovalent atoms in the molecular system. Its use reduces cutoff discontinuities
by avoiding splitting many of the largest charge separations found in typical molecules. Note
that this keyword does not rigorously implement the usual concept of a “neutral group” as
used in the literature with some versions of OPLS and other force fields. This option works
only for the simple charge-charge electrostatic potential; it does not affect bond dipole or
atomic multipole potentials.
NEWHESS [integer]
Sets the number of algorithmic iterations between recomputation of the Hessian matrix.
At present this keyword applies exclusively to optimizations using the truncated Newton
method. The default value in the absence of this keyword is 1, i.e., the Hessian is computed
on every iteration.
NEXTITER [integer]
Sets the iteration number to be used for the first iteration of the current computation. At
present this keyword applies to optimization procedures where its use can effect convergence
criteria, timing of restarts, and so forth. The default in the absence of this keyword is to take
the initial iteration as iteration 1.
NOARCHIVE
Causes Tinker molecular dynamics-based programs to write trajectory frames directly to “cy-
cle” files with a sequentially numbered file extension. The default, in the absence of this key-
word, is to implement the ARCHIVE behavior and write a single plain-text trajectory archive
file with the .arc format.
NONBONDTERM [NONE / ONLY]
Controls use of the nonbond potential energy terms. The nonbond terms include vdw, repul-
sion, dispersion, electrostatics and other potentials described by through-space interactions.
The NONE option turns off use of all nonbond potential energy terms. The ONLY option turns
off all potential energy terms except for these terms.
NODESCREEN
NOSYMMETRY
Forces the use of triclinic periodic boundary conditions and minimum image generation re-
gardless of any symmetry or equilvalent values in the periodic box or crystal lattice values.
Used to allow the possibility of symmetry breaking during calculations that begin from a
symmetric structure.
NOVERSION
Turns off the use of version numbers appended to the end of filenames as the method for
generating filenames for updated copies of an existing file. The presence of this keyword
results in direct use of input file names without a search for the highest available version, and
requires the entry of specific output file names in many additional cases. By default, in the
absence of this keyword, Tinker generates and attaches version numbers in a manner similar

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to the Digital OpenVMS operating system. For example, subsequent new versions of the file
molecule.xyz would be written first to the file molecule.xyz_2, then to molecule.xyz_3, etc.
OCTAHEDRON
Specifies that the periodic “box” is a truncated octahedron with maximal distance between
parallel faces across the periodic box as given by the A-AXIS keyword. The b-axis and c-
axis are set equal to the a-axis, the volume of the resulting truncated octahedron is half the
volume of the corresponding rectangular prism. All other unit cell and size-defining keywords
are ignored if the OCTAHEDRON keyword is present.
ONION-PROBE [real]
Sets the value in Angstroms of the solvent probe radius to be used in computing Born radii
via the Macromodel “onion” method applied to the Grycuk integral formulation. A default
value of zero is used in the absence of the CAVITY-PROBE keyword.
OPBEND [4 integers & 1 real]
Provides the values for a single out-of-plane bending potential parameter. The first integer
modifier is the atom class of the out-of-plane atom and the second integer is the atom class
of the central trigonal atom. The third and fourth integers give the atom classes of the two
remaining atoms attached to the trigonal atom. Values of zero for the third and fourth integers
are treated as wildcards, and can represent any atom type. The real number modifier gives
the force constant value for the out-of-plane angle. The default units for the force constant
are kcal/mole/radian^2, but this can be controlled via the OPBENDUNIT keyword.
OPBEND-CUBIC [real]
Sets the value of the cubic term in the Taylor series expansion form of the out-of-plane bend-
ing potential energy. The real number modifier gives the value of the coefficient as a multiple
of the quadratic coefficient. This term multiplied by the out-of-plane bending energy unit
conversion factor, the force constant, and the cube of the deviation of the out-of-plane angle
from zero gives the cubic contribution to the out-of-plane bending energy. The default value
in the absence of the OPBEND-CUBIC keyword is zero; i.e., the cubic out-of-plane bending
term is omitted.
OPBEND-PENTIC [real]
Sets the value of the fifth power term in the Taylor series expansion form of the out-of-plane
bending potential energy. The real number modifier gives the value of the coefficient as a
multiple of the quadratic coefficient. This term multiplied by the out-of-plane bending energy
unit conversion factor, the force constant, and the fifth power of the deviation of the out-
of-plane angle from zero gives the pentic contribution to the out-of-plane bending energy.
The default value in the absence of the OPBEND-PENTIC keyword is zero; i.e., the pentic
out-of-plane bending term is omitted.
OPBEND-QUARTIC [real]
Sets the value of the quartic term in the Taylor series expansion form of the out-of-plane
bending potential energy. The real number modifier gives the value of the coefficient as a
multiple of the quadratic coefficient. This term multiplied by the out-of-plane bending energy
unit conversion factor, the force constant, and the forth power of the deviation of the out-
of-plane angle from zero gives the quartic contribution to the out-of-plane bending energy.
The default value in the absence of the OPBEND-QUARTIC keyword is zero; i.e., the quartic
out-of-plane bending term is omitted.

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OPBEND-SEXTIC [real]
Sets the value of the sixth power term in the Taylor series expansion form of the out-of-plane
bending potential energy. The real number modifier gives the value of the coefficient as a
multiple of the quadratic coefficient. This term multiplied by the out-of-plane bending energy
unit conversion factor, the force constant, and the sixth power of the deviation of the out-
of-plane angle from zero gives the sextic contribution to the out-of-plane bending energy.
The default value in the absence of the OPBEND-SEXTIC keyword is zero; i.e., the sextic
out-of-plane bending term is omitted.
OPBENDTERM [NONE / ONLY]
Controls use of the out-of-plane bending potential energy term. In the absence of a modifying
option, this keyword turns on use of the potential. The NONE option turns off use of this
potential energy term. The ONLY option turns off all potential energy terms except for this
one.
OPBENDTYPE [W-D-C / Allinger]
Sets the type of angle to be used in the out-of-plane bending potential energy term. The
choices are to use the Wilson-Decius-Cross (W-D-C) formulation from vibrational spec-
troscopy, or the Allinger angle from the MM2/MM3 force fields. The default value in the
absence of the OPBENDTYPE keyword is to use the W-D-C angle.
OPBENDUNIT [real]
Sets the scale factor needed to convert the energy value computed by the out-of-plane bending
potential into units of kcal/mole. The correct value is force field dependent and typically
provided in the header of the master force field parameter file. The default of (Pi/180)^2 =
0.0003046 is used, if the OPBENDUNIT keyword is not given in the force field parameter file
or the keyfile.
OPDIST [4 integers & 1 real]
Provides the values for a single out-of-plane distance potential parameter. The first integer
modifier is the atom class of the central trigonal atom and the three following integer modi-
fiers are the atom classes of the three attached atoms. The real number modifier is the force
constant for the harmonic function of the out-of-plane distance of the central atom. The de-
fault units for the force constant are kcal/mole/Ang^2, but this can be controlled via the
OPDISTUNIT keyword.
OPDIST-CUBIC [real]
Sets the value of the cubic term in the Taylor series expansion form of the out-of-plane dis-
tance potential energy. The real number modifier gives the value of the coefficient as a mul-
tiple of the quadratic coefficient. This term multiplied by the out-of-plane distance energy
unit conversion factor, the force constant, and the cube of the deviation of the out-of-plane
distance from zero gives the cubic contribution to the out-of-plane distance energy. The de-
fault value in the absence of the OPDIST-CUBIC keyword is zero; i.e., the cubic out-of-plane
distance term is omitted.
OPDIST-PENTIC [real]
Sets the value of the fifth power term in the Taylor series expansion form of the out-of-plane
distance potential energy. The real number modifier gives the value of the coefficient as
a multiple of the quadratic coefficient. This term multiplied by the out-of-plane distance
energy unit conversion factor, the force constant, and the fifth power of the deviation of
the out-of-plane distance from zero gives the pentic contribution to the out-of-plane distance

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energy. The default value in the absence of the OPDIST-PENTIC keyword is zero; i.e., the
pentic out-of-plane distance term is omitted.
OPDIST-QUARTIC [real]
Sets the value of the quartic term in the Taylor series expansion form of the out-of-plane
distance potential energy. The real number modifier gives the value of the coefficient as
a multiple of the quadratic coefficient. This term multiplied by the out-of-plane distance
energy unit conversion factor, the force constant, and the forth power of the deviation of the
out-of-plane distance from zero gives the quartic contribution to the out-of-plane distance
energy. The default value in the absence of the OPDIST-QUARTIC keyword is zero; i.e., the
quartic out-of-plane distance term is omitted.
OPDIST-SEXTIC [real]
Sets the value of the sixth power term in the Taylor series expansion form of the out-of-
plane distance potential energy. The real number modifier gives the value of the coefficient
as a multiple of the quadratic coefficient. This term multiplied by the out-of-plane distance
energy unit conversion factor, the force constant, and the sixth power of the deviation of
the out-of-plane distance from zero gives the sextic contribution to the out-of-plane distance
energy. The default value in the absence of the OPDIST-SEXTIC keyword is zero; i.e., the
sextic out-of-plane distance term is omitted.
OPDISTTERM [NONE / ONLY]
Controls use of the out-of-plane distance potential energy term. In the absence of a modifying
option, this keyword turns on use of the potential. The NONE option turns off use of this
potential energy term. The ONLY option turns off all potential energy terms except for this
one.
OPDISTUNIT [real]
Sets the scale factor needed to convert the energy value computed by the out-of-plane dis-
tance potential into units of kcal/mole. The correct value is force field dependent and typ-
ically provided in the header of the master force field parameter file. The default value of
1.0 is used, if the OPDISTUNIT keyword is not given in the force field parameter file or the
keyfile.
OPENMP-THREADS [integer]
Sets the number of threads to be used in OpenMP parallelization of certain Tinker calcula-
tions. The default in the absence of the OPENMP-THREADS keyword is to set the number of
threads equal to the total number of CPU cores found for the computer being used.
OPT-COEFF
OVERWRITE
Causes Tinker programs, such as minimizations, that output intermediate coordinate sets to
create a single disk file for the intermediate results which is successively overwritten with
the new intermediate coordinates as they become available. This keyword is essentially the
opposite of the SAVECYCLE keyword.
PARAMETERS [file name]
Provides the name of the force field parameter file to be used for the current Tinker calcu-
lation. The standard file name extension for parameter files, .prm, is an optional part of the
file name modifier. The default in the absence of the PARAMETERS keyword is to look for
a parameter file with the same base name as the molecular system and ending in the .prm

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extension. If a valid parameter file is not found, the user will asked to provide a file name
interactively.
PCG-GUESS
PCG-NOGUESS
PCG-NOPRECOND
PCG-PEEK
PCG-PRECOND
PENETRATION
PEWALD-ALPHA [real]
Sets the value of the Ewald coefficient which controls the width of the Gaussian screening
charges during particle mesh Ewald summation for polarization interactions. In the absence
of the PEWALD-ALPHA keyword, the EWALD-ALPHA is used, or a value is chosen which
causes interactions outside the real-space cutoff to be below a fixed tolerance. For most
standard applications of polarization Ewald summation, the program default should be used.
PIATOM [1 integer & 3 reals]
Provides the values for the pisystem MO potential parameters for a single atom class belong-
ing to a pisystem.
PIBOND [2 integers & 2 reals]
Provides the values for the pisystem MO potential parameters for a single type of pisystem
bond.
PIBOND4 [2 integers & 2 reals]
Provides the values for the pisystem MO potential parameters for a single type of pisystem
bond contained in a 4-membered ring.
PIBOND5 [2 integers & 2 reals]
Provides the values for the pisystem MO potential parameters for a single type of pisystem
bond contained in a 5-membered ring.
PISYSTEM [integer list]
Sets the atoms within a molecule that are part of a conjugated pi-orbital system. The keyword
is followed on the same line by a list of atom numbers and/or atom ranges that constitute
the pi-system. The Allinger MM force fields use this information to set up an MO calculation
used to scale bond and torsion parameters involving pi-system atoms.
PITORS [2 integers & 1 real]
Provides the values for a single pi-orbital torsional angle potential parameter. The two in-
teger modifiers give the atom class numbers for the atoms involved in the central bond of
the torsional angle to be parameterized. The real modifier gives the value of the 2-fold
Fourier amplitude for the torsional angle between p-orbitals centered on the defined bond
atom classes. The default units for the stretch-torsion force constant can be controlled via the
PITORSUNIT keyword.
PITORSTERM [NONE / ONLY]
Controls use of the pi-orbital torsional angle potential energy term. In the absence of a
modifying option, this keyword turns on use of the potential. The NONE option turns off use

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of this potential energy term. The ONLY option turns off all potential energy terms except for
this one.
PITORSUNIT [real]
Sets the scale factor needed to convert the energy value computed by the pi-orbital torsional
angle potential into units of kcal/mole. The correct value is force field dependent and typ-
ically provided in the header of the master force field parameter file. The default value of
1.0 is used, if the PITORSUNIT keyword is not given in the force field parameter file or the
keyfile.
PME-GRID [3 integers]
Sets the dimensions of the reciprocal space grid used during particle mesh Ewald summation
for electrostatics. The three modifiers give the size along the X-, Y- and Z-axes, respectively. If
either the Y- or Z-axis dimensions are omitted, then they are set equal to the X-axis dimension.
The default in the absence of the PME-GRID keyword is to set the grid size along each axis to
the smallest power of 2, 3 and/or 5 which is at least as large as 1.2 times the axis length in
Angstoms.
PME-ORDER [integer]
Sets the order of the B-spline interpolation used during particle mesh Ewald summation for
partial charge or atomic multipole electrostatics. A default value of 5 is used in the absence
of the PME-ORDER keyword.
POLAR-12-INTRA [real]
Provides a multiplicative scale factor that is applied to polarization interactions between 1-2
connected atoms located in the same polarization group. The default value of 0.0 is used, if
the POLAR-12-INTRA keyword is not given in either the parameter file or the keyfile.
POLAR-12-SCALE [real]
Provides a multiplicative scale factor that is applied to polarization interactions between 1-2
connected atoms located in different polarization groups. The default value of 0.0 is used, if
the POLAR-12-SCALE keyword is not given in either the parameter file or the keyfile.
POLAR-13-INTRA [real]
Provides a multiplicative scale factor that is applied to polarization interactions between 1-3
connected atoms located in the same polarization group. The default value of 0.0 is used, if
the POLAR-13-INTRA keyword is not given in either the parameter file or the keyfile.
POLAR-13-SCALE [real]
Provides a multiplicative scale factor that is applied to polarization interactions between 1-3
connected atoms located in different polarization groups. The default value of 0.0 is used, if
the POLAR-13-SCALE keyword is not given in either the parameter file or the keyfile.
POLAR-14-INTRA [real]
Provides a multiplicative scale factor that is applied to polarization interactions between 1-4
connected atoms located in the same polarization group. The default value of 0.5 is used, if
the POLAR-14-INTRA keyword is not given in either the parameter file or the keyfile.
POLAR-14-SCALE [real]
Provides a multiplicative scale factor that is applied to polarization interactions between 1-4
connected atoms located in different polarization groups. The default value of 1.0 is used, if
the POLAR-14-SCALE keyword is not given in either the parameter file or the keyfile.

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POLAR-15-INTRA [real]
Provides a multiplicative scale factor that is applied to polarization interactions between 1-5
connected atoms located in the same polarization group. The default value of 1.0 is used, if
the POLAR-15-INTRA keyword is not given in either the parameter file or the keyfile.
POLAR-15-SCALE [real]
Provides a multiplicative scale factor that is applied to polarization interactions between 1-5
connected atoms located in different polarization groups. The default value of 1.0 is used, if
the POLAR-15-SCALE keyword is not given in either the parameter file or the keyfile.
POLAR-EPS [real]
Sets the convergence criterion applied during computation of self-consistent induced dipoles.
The calculation is deemed to have converged when the rms change in Debyes in the induced
dipole at all polarizable sites is less than the value specified with this keyword. The default
value in the absence of the keyword is 0.000001 Debyes.
POLAR-ITER
Sets the maximum number of conjugate gradient iterations to be used in the solution of the
self-consistent mutual induced dipoles. The default values in the absence of the keyword is
100 iterations.
POLAR-PREDICT [ASPC / GEAR / LSQR]
Turns on use of an induced dipole prediction method to accelerate convergence of self-
consistent induced dipoles. The Always Stable Predictor-Corrector (ASPC) method, a stan-
dard Gear extrapolation method (GEAR), and extrapolation based on a least squared predic-
tion (LSQR) are available as modifiers to the keyword. The default value if the keyword is
used without a modifier is ASPC. Use of POLAR-PREDICT biases the early stages of induced
dipole convergence, and should only be used when requesting tight convergence of 0.00001
or less via POLAR-EPS.
POLARIZABLE
POLARIZATION [DIRECT / MUTUAL]
Selects between the use of direct and mutual dipole polarization for force fields that incorpo-
rate the polarization term. The DIRECT modifier avoids an iterative calculation by using only
the permanent electric field in computation of induced dipoles. The MUTUAL option, which
is the default in the absence of the POLARIZATION keyword, iterates the induced dipoles to
self-consistency.
POLARIZE [1 integer, up to 3 reals & up to 8 integers]
Provides the values for a single atomic dipole polarizability parameter. The initial integer
modifier, if positive, gives the atom type number for which a polarizability parameter is to be
defined. If the first integer modifier is negative, then the parameter value to follow applies
only to the specific atom whose atom number is the negative of the modifier. The first real
number modifier gives the value of the dipole polarizability in Ang^3. The second real
number modifier, if present, gives the Thole damping value. A Thole value of zero implies
undamped polarization. If this modifier is not present, then charge penetration values will be
used for polarization damping, as in the HIPPO polarization model. The third real modifier, if
present, gives a direct field damping value only used with the AMOEBA+ polarization model.
The remaining integer modifiers list the atom type numbers of atoms directly bonded to the
current atom and which will be considered to be part of the current atom’s polarization group.

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If the parameter is for a specific atom, then the integers defining the polarization group are
ignored.
POLARIZETERM [NONE / ONLY]
Controls use of the atomic dipole polarization potential energy term. In the absence of a
modifying option, this keyword turns on use of the potential. The NONE option turns off use
of this potential energy term. The ONLY option turns off all potential energy terms except for
this one.
POLPAIR [2 integers & 2 reals]
Provides the values for the Thole damping of polarization for a single special heteroatomic
pair of atoms. The integer modifiers give the pair of atom type numbers for which special
Thole parameters are to be defined. The first real number modifier gives the original Thole
damping value. The optional second real number modifier gives the alternatve Thole damping
minimum value used to damp direct field polarization in selected models.
POLYMER-CUTOFF [real]
Sets the value of an additional cutoff parameter needed for infinite polymer systems. This
value must be set to less than half the minimal periodic box dimension and should be greater
than the largest possible interatomic distance that can be subject to scaling or exclusion as a
local electrostatic or van der Waals interaction. The default in the absence of the POLYMER-
CUTOFF keyword is 5.5 Angstroms.
POTENTIAL-ATOMS [integer list]
Sets the list of atoms whose grid points will be included in electrostatic potential calculations
and fitting. A grid point is considered to belong to the atom to which it is closest. Multiple
POTENTIAL-ATOMS lines can be present in the keyfile and are treated cumulatively. In the
absence of POTENTIAL-ATOMS keywords, all grid points are used.
POTENTIAL-FACTOR [real]
Provides a multiplicative scaling value to be applied to the van der Waals radii of atoms prior
to construction of the electrostatic potential grid surrounding a target system. The default
value used in the absence of the POTENTIAL-FACTOR keyword is 1.0.
POTENTIAL-FIT [integer list]
Sets the list of atoms whose partial charge or atomic multipole parameters will be allowed
to vary during electrostatic potential fitting. Multiple POTENTIAL-FIT lines can be present
in the keyfile and are treated cumulatively. In the absence of POTENTIAL-FIT keywords, all
atoms are used during the fitting procedure.
POTENTIAL-OFFSET [real]
Provides an additive offset value in Angstroms to be applied to the van der Waals radii of
atoms prior to construction of the electrostatic potential grid surrounding a target system.
The default value used in the absence of the POTENTIAL-OFFSET keyword is 1.0, meaning
that the closest shell of grid points will lie 1.0 Angstroms outside of the vdW radii.
POTENTIAL-SHELLS [integer[
Sets the number of radial shells of grid points used in the electrostatic potential grid surround-
ing a target system. A default value of 4 is used in the absence of the POTENTIAL-SHELLS
keyword.
POTENTIAL-SPACING [real]

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Sets the spacing in Angstroms for construction of the electrostatic potential grid, includ-
ing both the distance between shells of grid points and the average point-to-point distance
within a shell. The default value in the absence of the POTENTIAL-SPACING keyword is 0.35
Angstroms.
PPME-ORDER [integer]
Sets the order of the B-spline interpolation used during particle mesh Ewald summation for
polarization interactions. A default value of 5 is used in the absence of the PPME-ORDER
keyword.
PRINTOUT [integer]
Sets the number of iterations between writes of status information to the standard output for
iterative procedures such as minimizations. The default value in the absence of the keyword
is 1, i.e., the calculation status is given every iteration.
RADIUSRULE [ARITHMETIC / GEOMETRIC / CUBIC-MEAN]
Sets the functional form of the radius combining rule for heteroatomic van der Waals potential
energy interactions. The default in the absence of the RADIUSRULE keyword is to use the
arithmetic mean combining rule to get radii for heteroatomic interactions.
RADIUSSIZE [RADIUS / DIAMETER]
Determines whether the atom size values given in van der Waals parameters read from VDW
keyword statements are interpreted as atomic radius or diameter values. The default in the
absence of the RADIUSSIZE keyword is to assume that vdw size parameters are given as
radius values.
RADIUSTYPE [R-MIN / SIGMA]
Determines whether atom size values given in van der Waals parameters read from VDW
keyword statements are interpreted as potential minimum (Rmin) or LJ-style sigma values.
The default in the absence of the RADIUSTYPE keyword is to assume that vdw size parameters
are given as Rmin values.
RANDOMSEED [integer]
Followed by an integer value, sets the initial seed value for the random number generator
used by Tinker. Setting RANDOMSEED to the same value as an earlier run will allow exact
reproduction of the earlier calculation. (Note that this will not hold across different machine
types.) RANDOMSEED should be set to a positive integer less than about 2 billion. In the ab-
sence of the RANDOMSEED keyword the seed is chosen “randomly” based upon the number
of seconds that have elapsed in the current decade.
RATTLE [BONDS / ANGLES / DIATOMIC / TRIATOMIC / WATER]
Invokes the rattle algorithm, a velocity version of shake, on portions of a molecular system
during a molecular dynamic calculation. The RATTLE keyword can be followed by any of the
modifiers shown, in which case all occurrences of the modifier species are constrained at ideal
values taken from the bond and angle parameters of the force field in use. In the absence of
any modifier, RATTLE constrains all bonds to hydrogen atoms at ideal bond lengths.
RATTLE-DISTANCE [2 integers]
Allows the use of a holonomic constraint between the two atoms whose numbers are specified
on the keyword line. If the two atoms are involved in a covalent bond, then their distance
is constrained to the ideal bond length from the force field. For nonbonded atoms, the rattle
constraint is fixed at their distance in the input coordinate file.

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RATTLE-EPS
RATTLE-LINE [integer]
RATTLE-ORIGIN [integer]
RATTLE-PLANE [integer]
REACTIONFIELD [2 reals & 1 integer]
Provides parameters needed for the reaction field potential energy calculation. The two real
modifiers give the radius of the dielectric cavity and the ratio of the bulk dielectric outside
the cavity to that inside the cavity. The integer modifier gives the number of terms in the
reaction field summation to be used. In the absence of the REACTIONFIELD keyword, the
default values are a cavity of radius 1000000 Ang, a dielectric ratio of 80 and use of only the
first term of the reaction field summation.
REDUCE [real]
Specifies the fraction between zero and one by which the path between starting and final
conformational state will be shortened at each major cycle of the transition state location
algorithm implemented by the SADDLE program. This causes the path endpoints to move up
and out of the terminal structures toward the transition state region. In favorable cases, a
nonzero value of the REDUCE modifier can speed convergence to the transition state. The
default value in the absence of the REDUCE keyword is zero.
REMOVE-INERTIA [integer]
Specifies the number of molecular dynamics steps between removal of overall tranlational
and/or rotational motion of the system. The default value in the absence of the REMOVE-
INERTIA keyword is 100 steps.
REP-12-SCALE [real]
Provides a multiplicative scale factor that is applied to Pauli repulsion interactions between
1-2 connected atoms, i.e., atoms that are directly bonded. The default value of 0.0 is used to
omit 1-2 interactions, if the REP-12-SCALE keyword is not given in either the parameter file
or the keyfile.
REP-13-SCALE [real]
Provides a multiplicative scale factor that is applied to Pauli repulsion interactions between
1-3 connected atoms, i.e., atoms separated by two covalent bonds. The default value of
0.0 is used to omit 1-3 interactions, if the REP-13-SCALE keyword is not given in either the
parameter file or the keyfile.
REP-14-SCALE [real]
Provides a multiplicative scale factor that is applied to Pauli repulsion interactions between
1-4 connected atoms, i.e., atoms separated by three covalent bonds. The default value of 1.0
is used, if the REP-14-SCALE keyword is not given in either the parameter file or the keyfile.
REP-15-SCALE [real]
Provides a multiplicative scale factor that is applied to Pauli repulsion interactions between
1-5 connected atoms, i.e., atoms separated by three covalent bonds. The default value of 1.0
is used, if the REP-15-SCALE keyword is not given in either the parameter file or the keyfile.
REPULS-CUTOFF [real]
Sets the cutoff distance value in Angstroms for Pauli repulsion potential energy interactions.

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The energy for any pair of sites beyond the cutoff distance will be set to zero. Other keywords
can be used to select a smoothing scheme near the cutoff distance. The default cutoff distance
in the absence of the REPULS-CUTOFF keyword is 6.0 Angstroms.
REPULS-TAPER [real]
Modifies the cutoff window for Pauli repulsion energy interactions. It is similar in form and
action to the TAPER keyword, except that its value applies only to the Pauli repulsion poten-
tial. The default value in the absence of the REPULS-TAPER keyword is to begin the cutoff
window at 0.9 of the corresponding cutoff distance.
REPULSION
REPULSIONTERM [NONE / ONLY]
Controls use of the Pauli repulsion potential energy term. In the absence of a modifying
option, this keyword turns on use of the potential. The NONE option turns off use of this
potential energy term. The ONLY option turns off all potential energy terms except for this
one.
RESP-WEIGHT [real]
Provides a weight value for the restraint of partial charge and atomic multipole values during
electrostatic potential fitting. A value of 1.0 or larger gives a relatively strong restraint, while
a value of zero corresponds to no restraint. The actual weight applied is multiplicative, and
proportional to the square root of this keyword values. The default value in the absence of
the RESP-WEIGHT keyword is to use a value of 1.0.
RESPA-INNER [real]
RESPTYPE [ORIG / ZERO / NONE]
Provides the reference values for restraint of electrostatic parameters during potential fitting.
ORIG restrains the partial charges and atomic multipoles to their original values at the begin-
ning of the fitting procedure. ZERO restrains all electrostatic parameters to a value of zero,
in order to fit a model with the smallest reasonable parameter values. NONE removes the
restraint entirely. The default value in the absence of the RESPTYPE keyword is to restrain
the potential fit parameters to their original input values, i.e., to use ORIG.
RESTRAIN-ANGLE [3 integers & 3 reals]
Implements a flat-welled harmonic potential that can be used to restrain the angle between
three atoms to lie within a specified angle range. The integer modifiers contain the atom
numbers of the three atoms whose angle is to be restrained. The first real modifier is the
force constant in kcal/radian^2 for the restraint. The last two real modifiers give the lower
and upper bounds in degrees on the allowed angle values. If the angle lies between the lower
and upper bounds, the restraint potential is zero. Outside the bounds, the harmonic restraint
is applied. If the angle range modifiers are omitted, then the atoms are restrained to the angle
found in the input structure. If the force constant is also omitted, a default value of 10.0 is
used.
RESTRAIN-DISTANCE [2 integers & 3 reals]
Implements a flat-welled harmonic potential that can be used to restrain two atoms to lie
within a specified distance range. The integer modifiers contain the atom numbers of the two
atoms to be restrained. The first real modifier specifies the force constant in kcal/Ang^2 for
the restraint. The next two real modifiers give the lower and upper bounds in Angstroms on
the allowed distance range. If the interatomic distance lies between these lower and upper

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bounds, the restraint potential is zero. Outside the bounds, the harmonic restraint is applied.
If the distance range modifiers are omitted, then the atoms are restrained to the interatomic
distance found in the input structure. If the force constant is also omitted, a default value of
100.0 is used.
RESTRAIN-GROUPS [2 integers & 3 reals]
Implements a flat-welled harmonic distance restraint between the centers-of-mass of two
groups of atoms. The integer modifiers are the numbers of the two groups which must be
defined separately via the GROUP keyword. The first real modifier is the force constant in
kcal/Ang^2 for the restraint. The last two real modifiers give the lower and upper bounds
in Angstroms on the allowed intergroup center-of-mass distance values. If the distance range
modifiers are omitted, then the groups are restrained to the distance found in the input
structure. If the force constant is also omitted, a default value of 100.0 is used.
RESTRAIN-PLANE [X / Y / Z, 1 integer & 3 reals]
Provides the ability to restrain an individual atom to a specified plane orthogonal to a coordi-
nate axis. The first modifier gives the axis (X, Y or Z) perpendicular to the restraint plane. The
integer modifier contains the atom number of the atom to be restrained. The first real number
modifier gives the coordinate value to which the atom is restrained along the specified axis.
The second real modifier sets the force constant in kcal/Ang^2 for the harmonic restraint
potential. The final real modifier defines a range above and below the specified plane within
which the restraint value is zero. If the coordinate values along the restraint axis is omitted,
a value of 0.0 is assumed. If the force constant is omitted, a default value of 100.0 is used. If
the exclusion range is omitted, it is taken to be zero.
RESTRAIN-POSITION [1 integer & 5 reals, OR 2 integers & 2 reals]
Provides the ability to restrain an atom or group of atoms to specified coordinate positions.
An initial positive integer modifier contains the atom number of the atom to be restrained.
The first three real number modifiers give the X-, Y- and Z-coordinates to which the atom is
tethered. The fourth real modifier sets the force constant in kcal/Ang^2 for the harmonic
restraint potential. The final real modifier defines a sphere around the specified coordinates
within which the restraint value is zero. If the coordinates are omitted, then the atom is
restrained to the origin. If the force constant is omitted, a default value of 100.0 is used. If
the exclusion sphere radius is omitted, it is taken to be zero.
Alternatively, if the initial integer modifier is negative, then a second integer is read, followed
by two real number modifiers. All atoms in the range from the absolute value of the first
integer through the second integer are restrained to their current coordinates. The first real
modifier is the harmonic force constant in kcal/Ang^2, and the second real defines a sphere
around each atom within which the restraint value is zero. If the force constant is omitted, a
default value of 100.0 is used. If the exclusion sphere radius is omitted, it is taken to be zero.
RESTRAIN-TORSION [4 integers & 3 reals]
Implements a flat-welled harmonic potential that can be used to restrain the torsional angle
between four atoms to lie within a specified angle range. The initial integer modifiers contains
the atom numbers of the four atoms whose torsional angle, computed in the atom order
listed, is to be restrained. The first real modifier gives a force constant in kcal/radian^2
for the restraint. The last two real modifiers give the lower and upper bounds in degrees on
the allowed torsional angle values. The angle values given can wrap around across -180 and
+180 degrees. Outside the allowed angle range, the harmonic restraint is applied. If the

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angle range modifiers are omitted, then the atoms are restrained to the torsional angle found
in the input structure. If the force constant is also omitted, a default value of 1.0 is used.
RESTRAINTERM [NONE / ONLY]
Controls use of the restraint potential energy terms. In the absence of a modifying option, this
keyword turns on use of these potentials. The NONE option turns off use of these potential
energy terms. The ONLY option turns off all potential energy terms except for these terms.
ROTATABLE-BOND
RXNFIELDTERM [NONE / ONLY]
Controls use of the reaction field continuum solvation potential energy term. In the absence
of a modifying option, this keyword turns on use of the potential. The NONE option turns off
use of this potential energy term. The ONLY option turns off all potential energy terms except
for this one.
SADDLEPOINT
Allows Newton-style second derivative-based optimization routine used by NEWTON,
NEWTROT and other programs to converge to saddlepoints as well as minima on the po-
tential surface. By default, in the absence of the SADDLEPOINT keyword, checks are applied
that prevent convergence to stationary points having directions of negative curvature.
SAVE-CYCLE
Causes Tinker programs, such as minimizations and molecular dynamics, that output inter-
mediate coordinate sets to save each successive set to the next consecutively numbered cycle
file. The SAVE-CYCLE keyword is the opposite of the OVERWRITE keyword.
SAVE-FORCE
Causes Tinker molecular dynamics calculations to save the values of the force components
on each atom to a separate cycle file. These files are written whenever the atomic coordinate
snapshots are written during the dynamics run. Each atomic force file name contains as a
suffix the cycle number followed by the letter “f”.
SAVE-INDUCED
Causes Tinker molecular dynamics calculations that involve polarizable atomic multipoles to
save the values of the induced dipole components on each polarizable atom to a separate cycle
file. These files are written whenever the atomic coordinate snapshots are written during the
dynamics run. Each induced dipole file name contains as a suffix the cycle number followed
by the letter “u”.
SAVE-VECTS [integer]
Specifies the number of iterations between the saving of restart vectors during block iterative
determination of the low frequence vibrational modes. A default value of 10 is used for
SAVE-VECTS in the absence of the keyword.
SAVE-VELOCITY
Causes Tinker molecular dynamics calculations to save the values of the velocity components
on each atom to a separate cycle file. These files are written whenever the atomic coordinate
snapshots are written during the dynamics run. Each velocity file name contains as a suffix
the cycle number followed by the letter “v”.
SLOPEMAX [real]
Sets via its modifying value the maximum allowed size of the ratio between the current and

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initial projected gradients during the line search phase of conjugate gradient or truncated
Newton optimizations. If this ratio exceeds SLOPEMAX, then the initial step size is reduced
by a factor of 10. The default value is usually set to 10000.0 when not specified via the
SLOPEMAX keyword.
SMOOTHING [DEM / GDA / TOPHAT / STOPHAT]
Activates use of potential energy smoothing methods. Several variations are available de-
pending on the value of the modifier used: DEM= Diffusion Equation Method with a stan-
dard Gaussian kernel; GDA= Gaussian Density Annealing as proposed by the Straub group;
TOPHAT= a local DEM-like method using a finite range “tophat” kernel; STOPHAT= shifted
tophat smoothing.
SOLUTE [integers & 3 reals]
Provides values for a single implicit solvation parameter. The integer modifier gives the atom
type number for which solvation atom size parameters are to be defined. The three real
number modifiers give the values of the atomic diameter in Angstroms, for use in Poisson-
Boltzmann (APBS), ddCOSMO and Generalized Kirkwood (GK) calculations, respectively.
SOLVATE [ASP / SASA / ONION / STILL / HCT / OCB / ACE / GB / GB-HPMF / GK /
GK-HMPF / PB / PB-HMPF]
Turns on a continuum solvation free energy term during energy calculations when used with
standard force fields. Several algorithms are available based on the modifier used: ASP is
the Eisenberg-McLachlan ASP method using the Wesson-Eisenberg vacuum-to-water parame-
ters, SASA is the Ooi-Scheraga SASA method, ONION is the original 1990 Still “Onion-shell”
GB/SA method, STILL is the 1997 analytical GB/SA method from Still’s group, HCT is the
pairwise descreening method of Hawkins, Cramer and Truhlar, OBC is the Onufriev-Bashford-
Case method, ACE is the Analytical Continuum Electrostatics method from Karplus’ group, GB
is equivalent to the STILL modifier, GK is the Generalized Kirkwood method for polarizable
multipoles, and PB is a Poisson-Boltzmann method using APBS. The HPMF versions use Head-
Gordon’s Hydrophobic Potential of Mean Force method as the non-electrostatic component.
SOLVATETERM [NONE / ONLY]
Controls use of the macroscopic solvation potential energy term. In the absence of a modify-
ing option, this keyword turns on use of the potential. The NONE option turns off use of this
potential energy term. The ONLY option turns off all potential energy terms except for this
one.
SOLVENT-PRESSURE
SPACEGROUP [name]
Selects the space group to be used in manipulation of crystal unit cells and asymmetric units.
The name option must be chosen from one of the currently implemented space groups, which
include about 90 of the most common space groups out of the total of 230 possibilities.
STEEPEST-DESCENT
Forces the L-BFGS optimization routine used by the MINIMIZE program and other programs
to perform steepest descent minimization. This option can be useful in conjunction with small
step sizes for following minimum energy paths, but is generally inferior to the L-BFGS default
for most optimization purposes.
STEPMAX [real]
Sets via its modifying value the maximum size of an individual step during the line search

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phase of conjugate gradient or truncated Newton optimizations. The step size is computed
as the norm of the vector of changes in parameters being optimized. The default value de-
pends on the particular Tinker program, but is usually in the range from 1.0 to 5.0 when not
specified via the STEPMAX keyword.
STEPMIN [real]
Sets via its modifying value the minimum size of an individual step during the line search
phase of conjugate gradient or truncated Newton optimizations. The step size is computed as
the norm of the vector of changes in parameters being optimized. The default value is usually
set to about 10-16 when not specified via the STEPMIN keyword.
STRBND [3 integers & 2 reals]
Provides the values for a single stretch-bend cross term potential parameter. The integer
modifiers give the atom class numbers for the three kinds of atoms involved in the angle
which is to be defined. The real number modifiers give the force constant values for the first
bond (first two atom classes) with the angle, and the second bond with the angle, respectively.
The default units for the stretch-bend force constant are kcal/mole/Ang-radian, but this can
be controlled via the STRBNDUNIT keyword.
STRBNDTERM [NONE / ONLY]
Controls use of the bond stretching-angle bending cross term potential energy. In the absence
of a modifying option, this keyword turns on use of the potential. The NONE option turns off
use of this potential energy term. The ONLY option turns off all potential energy terms except
for this one.
STRBNDUNIT [real]
Sets the scale factor needed to convert the energy value computed by the bond stretching-
angle bending cross term potential into units of kcal/mole. The correct value is force field
dependent and typically provided in the header of the master force field parameter file. The
default value of (Pi/180) = 0.0174533 is used, if the STRBNDUNIT keyword is not given in
the force field parameter file or the keyfile.
STRTORS [2 integers & 1 real]
Provides the values for a single stretch-torsion cross term potential parameter. The two inte-
ger modifiers give the atom class numbers for the atoms involved in the central bond of the
torsional angles to be parameterized. The real modifier gives the value of the stretch-torsion
force constant for all torsional angles with the defined atom classes for the central bond. The
default units for the stretch-torsion force constant can be controlled via the STRTORUNIT
keyword.
STRTORTERM [NONE / ONLY]
Controls use of the bond stretching-torsional angle cross term potential energy. In the absence
of a modifying option, this keyword turns on use of the potential. The NONE option turns off
use of this potential energy term. The ONLY option turns off all potential energy terms except
for this one.
STRTORUNIT [real]
Sets the scale factor needed to convert the energy value computed by the bond stretching-
torsional angle cross term potential into units of kcal/mole. The correct value is force field
dependent and typically provided in the header of the master force field parameter file. The
default value of 1.0 is used, if the STRTORUNIT keyword is not given in the force field

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parameter file or the keyfile.

SURFACE-TENSION
TANH-CORRECTION
TAPER [real]
Allows modification of the cutoff windows for nonbonded potential energy interactions. The
nonbonded terms are smoothly reduced from their standard value at the beginning of the
cutoff window to zero at the far end of the window. The far end of the window is specified via
the CUTOFF keyword or its potential function specific variants. The modifier value supplied
with the TAPER keyword sets the beginning of the cutoff window. The modifier can be given
either as an absolute distance value in Angstroms, or as a fraction between zero and one of the
CUTOFF distance. The default value in the absence of the TAPER keyword ranges from 0.65
to 0.9 of the CUTOFF distance depending on the type of potential function. The windows are
implemented via polynomial-based switching functions, in some cases combined with energy
shifting.
TARGET-DIPOLE
TARGET-QUADRUPOLE
TAU-PRESSURE [real]
Sets the coupling time in picoseconds for the Groningen-style pressure bath coupling used to
control the system pressure during molecular dynamics calculations. A default value of 2.0 is
used for TAU-PRESSURE in the absence of the keyword.
TAU-TEMPERATURE [real]
Sets the coupling time in picoseconds for the Groningen-style temperature bath coupling used
to control the system temperature during molecular dynamics calculations. A default value
of 0.1 is used for TAU-TEMPERATURE in the absence of the keyword.
TCG-GUESS
TCG-NOGUESS
TCG-PEEK
THERMOSTAT [BUSSI / BERENDSEN / ANDERSEN / NOSE-HOOVER]
Selects a thermostat algorithm for use during molecular dynamics. Four modifiers are avail-
able: BUSSI is a Bussi-Parrinello stochastic coupling method, BERENSDEN is the original
Berendsen bath coupling method, ANDERSEN is the Andersen stochastic collision method,
and NOSE-HOOVER is a Nose-Hoover extended variable chain method. The default in the
absence of the THERMOSTAT keyword is to use the BUSSI method.
TORS-LAMBDA [real]
Sets the value of the lambda scaling parameters for torsional interactions during free energy
calculations and similar. The real number modifier sets the position along path from the initial
state (lambda=0) to the final state (lambda=1). Alternatively, this parameter can set the
state of annihilation for specified torsional interactions from none (lambda=1) to complete
(lambda=0). The torsions involved in the scaling are given separately via ROTATABLE-BOND
keywords.

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TORSION [4 integers & up to 6 real/real/integer triples]

Provides the values for a single torsional angle parameter. The first four integer modifiers
give the atom class numbers for the atoms involved in the torsional angle to be defined.
Each of the remaining triples of real/real/integer modifiers give the amplitude, phase offset
in degrees and periodicity of a particular torsional function term, respectively. Periodicities
through 6-fold are allowed for torsional parameters.
TORSION4 [4 integers & up to 6 real/real/integer triples]
Provides the values for a single torsional angle parameter specific to atoms in 4-membered
rings. The first four integer modifiers give the atom class numbers for the atoms involved in
the torsional angle to be defined. The remaining triples of real number and integer modifiers
operate as described above for the TORSION keyword.
TORSION5 [4 integers & up to 6 real/real/integer triples]
Provides the values for a single torsional angle parameter specific to atoms in 5-membered
rings. The first four integer modifiers give the atom class numbers for the atoms involved in
the torsional angle to be defined. The remaining triples of real number and integer modifiers
operate as described above for the TORSION keyword.
TORSIONTERM [NONE / ONLY]
Controls use of the torsional angle potential energy term. In the absence of a modifying
option, this keyword turns on use of the potential. The NONE option turns off use of this
potential energy term. The ONLY option turns off all potential energy terms except for this
one.
TORSIONUNIT [real]
Sets the scale factor needed to convert the energy value computed by the torsional angle
potential into units of kcal/mole. The correct value is force field dependent and typically
provided in the header of the master force field parameter file. The default value of 1.0 is
used, if the TORSIONUNIT keyword is not given in the force field parameter file or the keyfile.
TORTORS [7 integers, then multiple lines of up to 3 real triples]
Provides the values for a single torsion-torsion parameter. The first five integer modifiers
give the atom class numbers for the atoms involved in the two adjacent torsional angles to be
defined. The last two integer modifiers contain the number of data grid points along each axis
of the torsion-torsion map. For example, this value will be 13 for a 30 degree torsional angle
spacing, i.e., 360/30 = 12, but 13 values are required since data values for both -180 and
+180 degrees must be supplied. The subsequent lines contain triples of real numbers with
the values in degrees of the two torsional angles and the target energy value in kcal/mole.
One to three such triples can be present on each input line until all triples have been provided,
i.e., 13 x 13 = 169 triples for a 30 degree grid in each torsion.
TORTORTERM [NONE / ONLY]
Controls use of the torsion-torsion potential energy term. In the absence of a modifying
option, this keyword turns on use of the potential. The NONE option turns off use of this
potential energy term. The ONLY option turns off all potential energy terms except for this
one.
TORTORUNIT [real]
Sets the scale factor needed to convert the energy value computed by the torsion-torsion
potential into units of kcal/mole. The correct value is force field dependent and typically

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provided in the header of the master force field parameter file. The default value of 1.0 is
used, if the TORTORUNIT keyword is not given in the force field parameter file or the keyfile.
TRIAL-DISTANCE [CLASSIC / RANDOM / TRICOR / HAVEL integer / PAIRWISE integer]
Sets the method for selection of a trial distance matrix during distance geometry computa-
tions. The keyword takes a modifier that selects the method to be used. The HAVEL and
PAIRWISE modifiers also require an additional integer value that specifies the number of
atoms used in metrization and the percentage of metrization, respectively. The default in the
absence of this keyword is to use the PAIRWISE method with 100 percent metrization. Fur-
ther information on the various methods is given with the description of the Tinker distance
geometry program.
TRIAL-DISTRIBUTION [real]
Sets the initial value for the mean of the Gaussian distribution used to select trial distances
between the lower and upper bounds during distance geometry computations. The value
given must be between 0 and 1 which represent the lower and upper bounds respectively.
This keyword is rarely needed since Tinker will usually be able to choose a reasonable value
by default.
TRUNCATE
Causes all distance-based nonbond energy cutoffs to be sharply truncated to an energy of zero
at distances greater than the value set by the cutoff keyword(s) without use of any shifting,
switching or smoothing schemes. At all distances within the cutoff sphere, the full interaction
energy is computed.
UNWRAP-COORDS
Turns off the wrapping of atomic coordinates to enforce periodic boundary condiations in
output files during optimization or molecular dynamics. The keyword has no effect if periodic
boundary conditions are not in use. The default in the absence of the UNWRAP-COORDS
keyword is to wrap coordinates from molecular dynamics, but to leave coordinates from
optimization unwrapped.
UREY-CUBIC [real]
Sets the value of the cubic term in the Taylor series expansion form of the Urey-Bradley
potential energy. The real number modifier gives the value of the coefficient as a multiple
of the quadratic coefficient. The default value in the absence of the UREY-CUBIC keyword is
zero; i.e., the cubic Urey-Bradley term is omitted.
UREY-QUARTIC [real]
Sets the value of the quartic term in the Taylor series expansion form of the Urey-Bradley
potential energy. The real number modifier gives the value of the coefficient as a multiple of
the quadratic coefficient. The default value in the absence of the UREY-QUARTIC keyword is
zero; i.e., the quartic Urey-Bradley term is omitted.
UREYBRAD [3 integers & 2 reals]
Provides the values for a single Urey-Bradley cross term potential parameter. The integer
modifiers give the atom class numbers for the three kinds of atoms involved in the angle for
which a Urey-Bradley term is to be defined. The real number modifiers give the force constant
value for the term and the target value for the 1-3 distance in Angstroms. The default units
for the force constant are kcal/mole/Ang^2, but this can be controlled via the UREYUNIT
keyword.

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UREYBRADTERM [NONE / ONLY]

Controls use of the Urey-Bradley potential energy term. In the absence of a modifying option,
this keyword turns on use of the potential. The NONE option turns off use of this potential
energy term. The ONLY option turns off all potential energy terms except for this one.
UREYUNIT [real]
Sets the scale factor needed to convert the energy value computed by the Urey-Bradley poten-
tial into units of kcal/mole. The correct value is force field dependent and typically provided
in the header of the master force field parameter file. The default value of 1.0 is used, if the
UREYUNIT keyword is not given in the force field parameter file or the keyfile.
USOLVE-ACCEL [real]
Sets the multiplicative acceleration factor applied to the diagonal elements of the sparse
preconditioner used during conjugate gradient solution of induced dipoles. The default value
of 2.0 is used in the absence of the USOLVE-ACCEL keyword.
USOLVE-BUFFER [real]
Sets the size of the neighbor list buffer in Angstroms for the sparse conjugate gradient precon-
ditioner used in computing induced dipoles. This value is added to the actual cutoff distance
to determine which pairs will be kept on the neighbor list. The default value in the absence
of the USOLVE-BUFFER keyword is 2.0 Angstroms.
USOLVE-CUTOFF [real]
Sets the cutoff distance value in Angstroms for the sparse conjugate gradient preconditioner
used in computing induced dipoles. The default cutoff distance in the absence of the USOLVE-
CUTOFF keyword is 4.5 Angstroms.
USOLVE-DIAGONAL
Specifies only diagonal elements of the conjugate gradient preconditioner will be used during
computation of induced dipoles, i.e., all off-diagonal elements will be neglected. The default
in the absence of the USOLVE-DIAGONAL keyword is to include off-diagonal preconditioner
elements to the separately supplied cutoff distance.
USOLVE-LIST
Turns on pairwise neighbor lists for the sparse conjugate gradient preconditioner used to
accelerate computation of induced dipoles. This method will yield identical energetic results
to the standard double loop methods.
VALENCETERM [NONE / ONLY]
Controls use of the valence potential energy term. The valence terms include bond, angle,
torsion, out-of-plane bend and other potentials described by local bonded geometry. The
NONE option turns off use of all valence potential energy terms. The ONLY option turns off
all potential energy terms except for these terms.
VDW [1 integer & 3 reals]
Provides values for a single van der Waals parameter. The integer modifier, if positive, gives
the atom class number for which vdw parameters are to be defined. Note that vdw parameters
are given for atom classes, not atom types. The three real number modifiers give the values of
the atom size in Angstroms, homoatomic well depth in kcal/mole, and an optional reduction
factor for univalent atoms.
VDW-12-SCALE [real]

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Provides a multiplicative scale factor that is applied to van der Waals potential interactions
between 1-2 connected atoms, i.e., atoms that are directly bonded. The default value of 0.0
is used to omit 1-2 interactions, if the VDW-12-SCALE keyword is not given in either the
parameter file or the keyfile.
VDW-13-SCALE [real]
Provides a multiplicative scale factor that is applied to van der Waals potential interactions
between 1-3 connected atoms, i.e., atoms separated by two covalent bonds. The default value
of 0.0 is used to omit 1-3 interactions, if the VDW-13-SCALE keyword is not given in either
the parameter file or the keyfile.
VDW-14-SCALE [real]
Provides a multiplicative scale factor that is applied to van der Waals potential interactions
between 1-4 connected atoms, i.e., atoms separated by three covalent bonds. The default
value of 1.0 is used, if the VDW-14-SCALE keyword is not given in either the parameter file
or the keyfile.
VDW-15-SCALE [real]
Provides a multiplicative scale factor that is applied to van der Waals potential interactions
between 1-5 connected atoms, i.e., atoms separated by four covalent bonds. The default
value of 1.0 is used, if the VDW-15-SCALE keyword is not given in either the parameter file
or the keyfile.
VDW-ANNIHILATE
Specifies van der Waals interactions will be annihilated instead of decoupled during free
energy calculations based on the vdw “lambda” value. In decoupling the intra-ligand in-
teractions remain fully present regardless of the “lambda” value, while in annihilation the
“lambda” value is applied to intra-ligand interactions. The default in the absence of the VDW-
ANNIHILATE keyword is to decouple van der Waals interactions between the mutated atoms
or ligand and the rest of the system.
VDW-CORRECTION
Turns on the use of an isotropic long-range correction term to approximately account for van
der Waals interactions beyond the cutoff distance. This correction modifies the value of the
van der Waals energy and virial due to van der Waals interactions, but has no effect on the
gradient of the van der Waals energy.
VDW-CUTOFF [real]
Sets the cutoff distance value in Angstroms for van der Waals potential energy interactions.
The energy for any pair of van der Waals sites beyond the cutoff distance will be set to
zero. Other keywords can be used to select a smoothing scheme near the cutoff distance. The
default cutoff distance in the absence of the VDW-CUTOFF keyword is infinite for nonperiodic
systems and 9.0 for periodic systems.
VDW-LAMBDA [real]
Sets the value of the lambda scaling parameters for vdw interactions during free energy
calculations and similar. The real number modifier sets the position along path from the
initial state (lambda=0) to the final state (lambda=1). Alternatively, this parameter can
set the state of decoupling or annihilation for specified groups from none (lambda=1) to
complete (lambda=0). The groups involved in the scaling are given separately via LIGAND
or MUTATE keywords.

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VDW-LIST
Turns on pairwise neighbor lists for any of the van der Waals potentials. This method will
yield identical energetic results to the standard double loop method.
VDW-TAPER [real]
Allows modification of the cutoff windows for van der Waals potential energy interactions. It
is similar in form and action to the TAPER keyword, except that its value applies only to the
vdw potential. The default value in the absence of the VDW-TAPER keyword is to begin the
cutoff window at 0.9 of the vdw cutoff distance.
VDW14 [1 integer & 2 reals]
Provides values for a single van der Waals parameter for use in 1-4 nonbonded interactions.
The integer modifier, if positive, gives the atom class number for which vdw parameters are
to be defined. Note that vdw parameters are given for atom classes, not atom types. The two
real number modifiers give the values of the atom size in Angstroms and the homoatomic
well depth in kcal/mole. Reduction factors, if used, are carried over from the VDW keyword
for the same atom class.
VDWINDEX [CLASS / TYPE]
Specifies whether van der Waals parameters are provided for atom classes or atom types.
While most force fields are indexed by atom class, in OPLS models the vdW values are indexed
by atom type. inThe default in the absence of the VDWINDEX keyword is to index vdW
parameters by atom class.
VDWPAIR [2 integers & 2 reals]
Provides the values for the vdw parameters for a single special heteroatomic pair of atoms.
The integer modifiers give the pair of atom class numbers for which special vdw parameters
are to be defined. The two real number modifiers give the values of the minimum energy
contact distance in Angstroms and the well depth at the minimum distance in kcal/mole.
VDWTERM [NONE / ONLY]
Controls use of the van der Waals repulsion-dispersion potential energy term. In the absence
of a modifying option, this keyword turns on use of the potential. The NONE option turns off
use of this potential energy term. The ONLY option turns off all potential energy terms except
for this one.
VDWTYPE [LENNARD-JONES / BUCKINGHAM / BUFFERED-14-7 / MM3-HBOND /
GAUSSIAN]
Sets the functional form for the van der Waals potential energy term. The text modifier gives
the name of the functional form to be used. The GAUSSIAN modifier value implements a
two or four Gaussian fit to the corresponding Lennard-Jones function for use with potential
energy smoothing schemes. The default in the absence of the VDWTYPE keyword is to use
the standard two parameter Lennard-Jones function.
VERBOSE
Turns on printing of secondary and informational output during a variety of Tinker computa-
tions; a subset of the more extensive output provided by the DEBUG keyword.
VIB-ROOTS
VIB-TOLERANCE
VOLUME-MOVE [real]

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Specifies the maximum magnitude in Ang^3 of a trial change in the periodic box size when
using a Monte Carlo barostat. The default value of 100.0 Ang^3 is used in the absence of
the VOLUME-MOVE keyword.
VOLUME-SCALE [MOLECULAR / ATOMIC]
Specifies the type of coordinate scaling to be used when making trial periodic box volume
size changes during use of a Monte Carlo barostat. The MOLECULAR modifier enforces rigid
body translation of molecules based on center of mass, while the ATOMIC value treats all
coordinates independently. The default in the absence of the VOLUME-SCALE keyword is to
use MOLECULAR scaling.
VOLUME-TRIAL [integer]
Specifies the average number of molecular dynamics steps between attempts to change the
periodic box size when using a Monte Carlo barostat. The default value of 25 steps is used in
the absence of the VOLUME-TRIAL keyword.
WALL [real]
Sets the radius of a spherical boundary used to maintain droplet boundary conditions. The
real modifier specifies the desired approximate radius of the droplet. In practice, an artificial
van der Waals wall is constructed at a fixed buffer distance of 2.5 Angstroms outside the
specified radius. The effect is that atoms which attempt to move outside the region defined
by the droplet radius will be forced toward the center.
WRAP-COORDS
Turns on the wrapping of atomic coordinates to enforce periodic boundary condiations in
output files during optimization or molecular dynamics. The keyword has no effect if peri-
odic boundary conditions are not in use. The default in the absence of the WRAP-COORDS
keyword is to wrap coordinates from molecular dynamics, but to leave coordinates from op-
timization unwrapped.
WRITEOUT [integer]
Sets the number of iterations between writes of intermediate results (such as the current
coordinates) to disk file(s) for iterative procedures such as minimizations. The default value
in the absence of the keyword is 1, i.e., the intermediate results are written to file on every
iteration. Whether successive intermediate results are saved to new files or replace previously
written intermediate results is controlled by the OVERWRITE and SAVE-CYCLE keywords.
X-AXIS [real]
Sets the value of the a-axis length for a crystal unit cell, or, equivalently, the X-axis length for
a periodic box. The length value in Angstroms is provided following the keyword. Equivalent
to the A-AXIS keyword.
Y-AXIS [real]
Sets the value of the b-axis length for a crystal unit cell, or, equivalently, the Y-axis length
for a periodic box. The length value in Angstroms is provided following the keyword. If the
keyword is absent, the Y-axis length is set equal to the X-axis length. Equivalent to the B-AXIS
keyword.
Z-AXIS [real]
Sets the value of the c-axis length for a crystal unit cell, or, equivalently, the Z-axis length
for a periodic box. The length value in Angstroms is provided following the keyword. If the

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keyword is absent, the Z-axis length is set equal to the X-axis length. Equivalent to the C-AXIS
keyword.

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 CHAPTER

NINE

ROUTINES & FUNCTIONS

The distribution version of the Tinker package contains over 1000 separate programs, subroutines
and functions. This section contains a brief description of the purpose of most of these code units.
Further information can be found in the comments located at the top of each source code file.
ACTIVE Subroutine
“active” sets the list of atoms that are used during each potential energy function calculation
ADDBASE Subroutine
“addbase” builds the Cartesian coordinates for a single nucleic acid base; coordinates are read from
the Protein Data Bank file or found from internal coordinates, then atom types are assigned and
connectivity data generated
ADDBOND Subroutine
“addbond” adds entries to the attached atoms list in order to generate a direct connection between
two atoms
ADDIONS Subroutine
“addions” takes a currently defined solvated system and places ions, with removal of solvent
molecules
ADDSIDE Subroutine
“addside” builds the Cartesian coordinates for a single amino acid side chain; coordinates are read
from the Protein Data Bank file or found from internal coordinates, then atom types are assigned
and connectivity data generated
ADJACENT Function
“adjacent” finds an atom connected to atom “i1” other than atom “i2”; if no such atom exists, then
the closest atom in space is returned
ADJUST Subroutine
“adjust” modifies site bounds on the PME grid and returns an offset into the B-spline coefficient
arrays
ALCHEMY Program

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“alchemy” computes the free energy difference corresponding to a small perturbation by Boltz-
mann weighting the potential energy difference over a number of sample states; current version
(incorrectly) considers the charge energy to be intermolecular in finding the perturbation energies
ALFCX Subroutine
“alfcx” builds the alpha complex based on the weighted Delaunay triangulation used by UnionBall
ALF_EDGE Subroutine
“alf_edge” checks if an edge belongs to the alpha complex; computes the radius of the sphere
orthogonal to the two balls that define the edge, if this radius is smaller than alpha then the edge
belongs to the alpha complex
ALF_TETRA Subroutine
“alf_tetra” computes the radius of the sphere orthogonal to the four spheres that define a tetrahe-
dron
ALF_TRIG Subroutine
“alf_trig” checks if whether a triangle belongs to the alpha complex; computes the radius of the
sphere orthogonal to 5h3 three balls defining the triangle; if this radius is smaller than alpha the
triangle belongs to the alpha complex
ALTELEC Subroutine
“altelec” constructs mutated electrostatic parameters based on the lambda mutation parameter
“elambda”
ALTERCHG Subroutine
“alterchg” calculates the change in atomic partial charge or monopole values due to bond and angle
charge flux coupling
ALTERPOL Subroutine
“alterpol” finds an output set of atomic multipole parameters which when used with an intergroup
polarization model will give the same electrostatic potential around the molecule as the input set
of multipole parameters with all atoms in one polarization group
ALTSOLV Subroutine
“altsolv” constructs mutated implicit solvation parameters based on the lambda mutation parameter
“elambda”
ALTTORS Subroutine
“alttors” constructs mutated torsional parameters based on the lambda mutation parameter
“tlambda”
AMBERYZE Subroutine
“amberyze” prints the force field parameters in a format needed by the Amber setup protocol for
using AMOEBA within Amber
ANALYSIS Subroutine

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“analysis” calls the series of routines needed to calculate the potential energy and perform energy
partitioning analysis in terms of type of interaction or atom number
ANALYZE Program
“analyze” computes and displays the total potential energy; options are provided to display sys-
tem and force field info, partition the energy by atom or by potential function type, show force
field parameters by atom; output the large energy interactions and find electrostatic and inertial
properties
ANGCHG Subroutine
“angchg” computes modifications to atomic partial charges or monopoles due to angle bending
using a charge flux formulation
ANGGUESS Function
“angguess” sets approximate angle bend force constants based on atom type and connected atoms
ANGLES Subroutine
“angles” finds the total number of bond angles and stores the atom numbers of the atoms defining
each angle; for each angle to a trivalent central atom, the third bonded atom is stored for use in
out-of-plane bending
ANNEAL Program
“anneal” performs a simulated annealing protocol by means of variable temperature molecular
dynamics using either linear, exponential or sigmoidal cooling schedules
ANORM Function
“anorm” finds the norm (length) of a vector; used as a service routine by the Connolly surface area
and volume computation
APBSEMPOLE Subroutine
APBSFINAL Subroutine
APBSINDUCE Subroutine
APBSINITIAL Subroutine
APBSNLINDUCE Subroutine
ARCEDIT Program
“arcedit” is a utility program for coordinate files which concatenates multiple coordinate sets into
a new archive or performs any of several manipulations on an existing archive
ASET Subroutine
“aset” computes by recursion the A functions used in the evaluation of Slater-type (STO) overlap
integrals
ATOMYZE Subroutine
“atomyze” prints the potential energy components broken down by atom and to a choice of preci-
sion

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ATTACH Subroutine
“attach” generates lists of 1-3, 1-4 and 1-5 connectivities starting from the previously determined
list of attached atoms (ie, 1-2 connectivity)
AUXINIT Subroutine
“auxinit” initializes auxiliary variables and settings for inertial extended Lagrangian induced dipole
prediction
AVGPOLE Subroutine
“avgpole” condenses the number of multipole atom types based upon atoms with equivalent at-
tachments and additional user specified sets of equivalent atoms
BALL_DSURF Subroutine
“ball_dsurf” computes the weighted surface area of a union of spheres as well as its derivatives
with respect to the distances between the sphere centers
BALL_DVOL Subroutine
“ball_dvol” computes the weighted surface area of a union of spheres and the weighted volume of
the corresponding union of balls, as well as their derivatives with respect to distances between the
sphere centers
BALL_SURF Subroutine
“ball_surf” computes the weighted accessible surface area of a union of spheres
BALL_VOL Subroutine
“ball_vol” computes the weighted surface area of a union of spheres and the weighted excluded
volume of the corresponding union of balls
BAOAB Subroutine
“baoab” implements a constrained stochastic dynamics time step using the geodesic BAOAB scheme
BAR Program
“bar” computes the free energy, enthalpy and entropy difference between two states via Zwanzig
free energy perturbation (FEP) and Bennett acceptance ratio (BAR) methods
BARCALC Subroutine
BASEFILE Subroutine
“basefile” extracts from an input filename the portion consisting of any directory name and the base
filename; also reads any keyfile and sets information level values
BCUCOF Subroutine
“bcucof” determines the coefficient matrix needed for bicubic interpolation of a function, gradients
and cross derivatives
BCUINT Subroutine
“bcuint” performs a bicubic interpolation of the function value on a 2D spline grid

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BCUINT1 Subroutine
“bcuint1” performs a bicubic interpolation of the function value and gradient along the directions
of a 2D spline grid
BCUINT2 Subroutine
“bcuint2” performs a bicubic interpolation of the function value, gradient and Hessian along the
directions of a 2D spline grid
BEEMAN Subroutine
“beeman” performs a single molecular dynamics time step via the Beeman multistep recursion
formula; uses original coefficients or Bernie Brooks’ “Better Beeman” values
BETACF Function
“betacf” computes a rapidly convergent continued fraction needed by routine “betai” to evaluate
the cumulative Beta distribution
BETAI Function
“betai” evaluates the cumulative Beta distribution function as the probability that a random variable
from a distribution with Beta parameters “a” and “b” will be less than “x”
BIGBLOCK Subroutine
“bigblock” replicates the coordinates of a single unit cell to give a larger unit cell as a block of
repeated units
BIOSORT Subroutine
“biosort” renumbers and formats biotype parameters used to convert biomolecular structure into
force field atom types
BITORS Subroutine
“bitors” finds the total number of bitorsions as pairs of adjacent torsional angles, and the numbers
of the five atoms defining each bitorsion
BMAX Function
“bmax” computes the maximum order of the B functions needed for evaluation of Slater-type (STO)
overlap integrals
BNDCHG Subroutine
“bndchg” computes modifications to atomic partial charges or monopoles due to bond stretch using
a charge flux formulation
BNDERR Function
“bnderr” is the distance bound error function and derivatives; this version implements the origi-
nal and Havel’s normalized lower bound penalty, the normalized version is preferred when lower
bounds are small (as with NMR NOE restraints), the original penalty is needed if large lower bounds
are present
BNDGUESS Function

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“bndguess” sets approximate bond stretch force constants based on atom type and connected atoms
BONDS Subroutine
“bonds” finds the total number of covalent bonds and stores the atom numbers of the atoms defining
each bond
BORN Subroutine
“born” computes the Born radius of each atom for use with the various implicit solvation models
BORN1 Subroutine
“born1” computes derivatives of the Born radii with respect to atomic coordinates and increments
total energy derivatives and virial components for potentials involving Born radii
BOUNDS Subroutine
“bounds” finds the center of mass of each molecule and translates any stray molecules back into
the periodic box
BOXMIN Subroutine
“boxmin” uses minimization of valence and vdw potential energy to expand and refine a collection
of solvent molecules in a periodic box
BOXMIN1 Function
“boxmin1” is a service routine that computes the energy and gradient during refinement of a peri-
odic box
BSET Subroutine
“bset” computes by downward recursion the B functions used in the evaluation of Slater-type (STO)
overlap integrals
BSPLGEN Subroutine
“bsplgen” gets B-spline coefficients and derivatives for a single PME atomic site along a particular
direction
BSPLINE Subroutine
“bspline” calculates the coefficients for an n-th order B-spline approximation
BSPLINE_FILL Subroutine
“bspline_fill” finds B-spline coefficients and derivatives for PME atomic sites along the fractional
coordinate axes
BSSTEP Subroutine
“bsstep” takes a single Bulirsch-Stoer step with monitoring of local truncation error to ensure accu-
racy
BUSSI Subroutine
“bussi” performs a single molecular dynamics time step via the Bussi-Parrinello isothermal-isobaric
algorithm

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CALENDAR Subroutine
“calendar” returns the current time as a set of integer values representing the year, month, day,
hour, minute and second
CART_TO_FRAC Subroutine
“cart_to_frac” computes a transformation matrix to convert a multipole object in Cartesian coordi-
nates to fractional
CBUILD Subroutine
“cbuild” performs a complete rebuild of the partial charge electrostatic neighbor list for all sites
CELLANG Subroutine
“cellang” computes atomic coordinates and unit cell parameters from fractional coordinates and
lattice vectors
CELLATOM Subroutine
“cellatom” completes the addition of a symmetry related atom to a unit cell by updating the atom
type and attachment arrays
CENTER Subroutine
“center” moves the weighted centroid of each coordinate set to the origin during least squares
superposition
CERROR Subroutine
“cerror” is the error handling routine for the Connolly surface area and volume computation
CFFTB Subroutine
“cfftb” computes the backward complex discrete Fourier transform, the Fourier synthesis
CFFTB1 Subroutine
CFFTF Subroutine
“cfftf” computes the forward complex discrete Fourier transform, the Fourier analysis
CFFTF1 Subroutine
CFFTI Subroutine
“cffti” initializes arrays used in both forward and backward transforms; “ifac” is the prime factor-
ization of “n”, and “wsave” contains a tabulation of trigonometric functions
CFFTI1 Subroutine
CHIRER Function
“chirer” computes the chirality error and its derivatives with respect to atomic Cartesian coordinates
as a sum the squares of deviations of chiral volumes from target values
CHKANGLE Subroutine
“chkangle” tests angles to be constrained for their presence in small rings and removes constraints
that are redundant

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CHKAROM Function
“chkatom” tests for the presence of a specified atom as a member of an aromatic ring
CHKPOLE Subroutine
“chkpole” inverts atomic multipole moments as necessary at sites with chiral local reference frame
definitions
CHKRING Subroutine
“chkring” tests an atom or a set of connected atoms for their presence within a single 3- to 6-
membered ring
CHKSIZE Subroutine
“chksize” computes a measure of overall global structural expansion or compaction from the num-
ber of excess upper or lower bounds matrix violations
CHKSOCKET Subroutine
CHKSYMM Subroutine
“chksymm” examines the current coordinates for linearity, planarity, an internal mirror plane or
center of inversion
CHKTREE Subroutine
“chktree” tests a minimum energy structure to see if it belongs to the correct progenitor in the
existing map
CHKTTOR Subroutine
“chkttor” tests the attached atoms at a torsion-torsion central site and inverts the angle values if
the site is chiral
CHKXYZ Subroutine
“chkxyz” finds any pairs of atoms with identical Cartesian coordinates, and prints a warning mes-
sage
CHOLESKY Subroutine
“cholesky” uses a modified Cholesky method to solve the linear system Ax = b, returning “x” in
“b”; “A” is a real symmetric positive definite matrix with its upper triangle (including the diagonal)
stored by rows
CIRPLN Subroutine
“cirpln” determines the points of intersection between a specified circle and plane
CJKM Function
“cjkm” computes the coefficients of spherical harmonics expressed in prolate spheroidal coordinates
CLIGHT Subroutine
“clight” performs a complete rebuild of the partial charge pair neighbor list for all sites using the
method of lights

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CLIMBER Subroutine
CLIMBRGD Subroutine
CLIMBROT Subroutine
CLIMBTOR Subroutine
CLIMBXYZ Subroutine
CLIST Subroutine
“clist” performs an update or a complete rebuild of the nonbonded neighbor lists for partial charges
CLUSTER Subroutine
“cluster” gets the partitioning of the system into groups and stores a list of the group to which each
atom belongs
CMP_TO_FMP Subroutine
“cmp_to_fmp” transforms the atomic multipoles from Cartesian to fractional coordinates
COLUMN Subroutine
“column” takes the off-diagonal Hessian elements stored as sparse rows and sets up indices to allow
column access
COMMAND Subroutine
“command” uses the standard Unix-like iargc/getarg routines to get the number and values of
arguments specified on the command line at program runtime
COMPRESS Subroutine
“compress” transfers only the non-buried tori from the temporary tori arrays to the final tori arrays
CONNECT Subroutine
“connect” sets up the attached atom arrays starting from a set of internal coordinates
CONNOLLY Subroutine
“connolly” uses the algorithms from the AMS/VAM programs of Michael Connolly to compute the
analytical molecular surface area and volume of a collection of spherical atoms; thus it implements
Fred Richards’ molecular surface definition as a set of analytically defined spherical and toroidal
polygons
CONNYZE Subroutine
“connyze” prints information onconnected atoms as lists of all atom pairs that are 1-2 through 1-5
interactions
CONTACT Subroutine
“contact” constructs the contact surface, cycles and convex faces
CONTROL Subroutine
“control” gets initial values for parameters that determine the output style and information level
provided by Tinker

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COORDS Subroutine
“coords” converts the three principal eigenvalues/vectors from the metric matrix into atomic coor-
dinates, and calls a routine to compute the rms deviation from the bounds
CORRELATE Program
“correlate” computes the time correlation function of some user-supplied property from individual
snapshot frames taken from a molecular dynamics or other trajectory
CREATEJVM Subroutine
CREATESERVER Subroutine
CREATESYSTEM Subroutine
CREATEUPDATE Subroutine
CRYSTAL Program
“crystal” is a utility which converts between fractional and Cartesian coordinates, and can generate
full unit cells from asymmetric units
CSPLINE Subroutine
“cspline” computes the coefficients for a periodic interpolating cubic spline
CUTOFFS Subroutine
“cutoffs” initializes and stores spherical energy cutoff distance windows, Hessian element and
Ewald sum cutoffs, and allocates pairwise neighbor lists
CYTSY Subroutine
“cytsy” solves a system of linear equations for a cyclically tridiagonal, symmetric, positive definite
matrix
CYTSYP Subroutine
“cytsyp” finds the Cholesky factors of a cyclically tridiagonal symmetric, positive definite matrix
given by two vectors
CYTSYS Subroutine
“cytsys” solves a cyclically tridiagonal linear system given the Cholesky factors
D1D2 Function
“d1d2” is a utility function used in computation of the reaction field recursive summation elements
DAMPDIR Subroutine
“dampdir” generates coefficients for the direct field damping function for powers of the interatomic
distance
DAMPEWALD Subroutine
“dampewald” generates coefficients for Ewald error function damping for powers of the interatomic
distance
DAMPMUT Subroutine

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“dampmut” generates coefficients for the mutual field damping function for powers of the inter-
atomic distance
DAMPPOLAR Subroutine
“damppolar” generates coefficients for the charge penetration damping function used for polariza-
tion interactions
DAMPPOLE Subroutine
“damppole” generates coefficients for the charge penetration damping function for powers of the
interatomic distance
DAMPPOT Subroutine
“damppot” generates coefficients for the charge penetration damping function used for the electro-
static potential
DAMPREP Subroutine
“damprep” generates coefficients for the Pauli repulsion damping function for powers of the inter-
atomic distance
DAMPTHOLE Subroutine
“dampthole” finds coefficients for the original Thole damping function used by AMOEBA and for
mutual polarization by AMOEBA+
DAMPTHOLED Subroutine
“damptholed” finds coefficients for the original Thole damping function used by AMOEBA or for
the alternate direct polarization damping used by AMOEBA+
DBUILD Subroutine
“dbuild” performs a complete rebuild of the damped dispersion neighbor list for all sites
DCFLUX Subroutine
“dcflux” takes as input the electrostatic potential at each atomic site and calculates gradient chain
rule corrections due to charge flux coupled with bond stretching and angle bending
DEFLATE Subroutine
“deflate” uses the power method with deflation to compute the few largest eigenvalues and eigen-
vectors of a symmetric matrix
DELETE Subroutine
“delete” removes a specified atom from the Cartesian coordinates list and shifts the remaining
atoms
DEPTH Function
DESTROYJVM Subroutine
DESTROYSERVER Subroutine
DFIELD0A Subroutine

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“dfield0a” computes the direct electrostatic field due to permanent multipole moments via a double
loop
DFIELD0B Subroutine
“dfield0b” computes the direct electrostatic field due to permanent multipole moments via a pair
list
DFIELD0C Subroutine
“dfield0c” computes the mutual electrostatic field due to permanent multipole moments via Ewald
summation
DFIELD0D Subroutine
“dfield0d” computes the direct electrostatic field due to permanent multipole moments for use with
with generalized Kirkwood implicit solvation
DFIELD0E Subroutine
“dfield0e” computes the direct electrostatic field due to permanent multipole moments for use with
in Poisson-Boltzmann
DFIELDI Subroutine
“dfieldi” computes the electrostatic field due to permanent multipole moments
DFTMOD Subroutine
“dftmod” computes the modulus of the discrete Fourier transform of “bsarray” and stores it in
“bsmod”
DIAGBLK Subroutine
“diagblk” performs diagonalization of the Hessian for a block of atoms within a larger system
DIAGQ Subroutine
“diagq” is a matrix diagonalization routine which is derived from the classical given, housec, and
eigen algorithms with several modifications to increase efficiency and accuracy
DIFFEQ Subroutine
“diffeq” performs the numerical integration of an ordinary differential equation using an adaptive
stepsize method to solve the corresponding coupled first-order equations of the general form dyi/dx
= f(x,y1,. . . ,yn) for yi = y1,. . . ,yn
DIFFUSE Program
“diffuse” finds the self-diffusion constant for a homogeneous liquid via the Einstein relation from a
set of stored molecular dynamics frames; molecular centers of mass are unfolded and mean squared
displacements are computed versus time separation
DIST2 Function
“dist2” finds the distance squared between two points; used as a service routine by the Connolly
surface area and volume computation
DISTGEOM Program

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“distgeom” uses a metric matrix distance geometry procedure to generate structures with interpoint
distances that lie within specified bounds, with chiral centers that maintain chirality, and with
torsional angles restrained to desired values; the user also has the ability to interactively inspect
and alter the triangle smoothed bounds matrix prior to embedding
DLIGHT Subroutine
“dlight” performs a complete rebuild of the damped dispersion pair neighbor list for all sites using
the method of lights
DLIST Subroutine
“dlist” performs an update or a complete rebuild of the nonbonded neighbor lists for damped
dispersion sites
DMDUMP Subroutine
“dmdump” puts the distance matrix of the final structure into the upper half of a matrix, the dis-
tance of each atom to the centroid on the diagonal, and the individual terms of the bounds errors
into the lower half of the matrix
DOCUMENT Program
“document” generates a formatted description of all the routines and modules, an index of routines
called by each source file, a list of all valid keywords, a list of include file dependencies as needed
by a Unix-style Makefile, or a formatted force field parameter summary
DOT Function
“dot” finds the dot product of two vectors
DSTMAT Subroutine
“dstmat” selects a distance matrix containing values between the previously smoothed upper and
lower bounds; the distance values are chosen from uniform distributions, in a triangle correlated
fashion, or using random partial metrization
DYNAMIC Program
“dynamic” computes a molecular or stochastic dynamics trajectory in one of the standard statistical
mechanical ensembles and using any of several possible integration methods
EANGANG Subroutine
“eangang” calculates the angle-angle potential energy
EANGANG1 Subroutine
“eangang1” calculates the angle-angle potential energy and first derivatives with respect to Carte-
sian coordinates
EANGANG2 Subroutine
“eangang2” calculates the angle-angle potential energy second derivatives with respect to Cartesian
coordinates using finite difference methods
EANGANG2A Subroutine

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“eangang2a” calculates the angle-angle first derivatives for a single interaction with respect to
Cartesian coordinates; used in computation of finite difference second derivatives
EANGANG3 Subroutine
“eangang3” calculates the angle-angle potential energy; also partitions the energy among the atoms
EANGLE Subroutine
“eangle” calculates the angle bending potential energy; projected in-plane angles at trigonal cen-
ters, special linear or Fourier angle bending terms are optionally used
EANGLE1 Subroutine
“eangle1” calculates the angle bending potential energy and the first derivatives with respect to
Cartesian coordinates; projected in-plane angles at trigonal centers, special linear or Fourier angle
bending terms are optionally used
EANGLE2 Subroutine
“eangle2” calculates second derivatives of the angle bending energy for a single atom using a
mixture of analytical and finite difference methods; projected in-plane angles at trigonal centers,
special linear or Fourier angle bending terms are optionally used
EANGLE2A Subroutine
“eangle2a” calculates bond angle bending potential energy second derivatives with respect to Carte-
sian coordinates
EANGLE2B Subroutine
“eangle2b” computes projected in-plane bending first derivatives for a single angle with respect to
Cartesian coordinates; used in computation of finite difference second derivatives
EANGLE3 Subroutine
“eangle3” calculates the angle bending potential energy, also partitions the energy among the
atoms; projected in-plane angles at trigonal centers, spceial linear or Fourier angle bending terms
are optionally used
EANGTOR Subroutine
“eangtor” calculates the angle-torsion potential energy
EANGTOR1 Subroutine
“eangtor1” calculates the angle-torsion energy and first derivatives with respect to Cartesian coor-
dinates
EANGTOR2 Subroutine
“eangtor2” calculates the angle-torsion potential energy second derivatives with respect to Carte-
sian coordinates
EANGTOR3 Subroutine
“eangtor3” calculates the angle-torsion potential energy; also partitions the energy terms among
the atoms

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EBOND Subroutine
“ebond” calculates the bond stretching energy
EBOND1 Subroutine
“ebond1” calculates the bond stretching energy and first derivatives with respect to Cartesian coor-
dinates
EBOND2 Subroutine
“ebond2” calculates second derivatives of the bond stretching energy for a single atom at a time
EBOND3 Subroutine
“ebond3” calculates the bond stretching energy; also partitions the energy among the atoms
EBUCK Subroutine
“ebuck” calculates the Buckingham exp-6 van der Waals energy
EBUCK0A Subroutine
“ebuck0a” calculates the Buckingham exp-6 van der Waals energy using a pairwise double loop
EBUCK0B Subroutine
“ebuck0b” calculates the Buckingham exp-6 van der Waals energy using the method of lights
EBUCK0C Subroutine
“ebuck0c” calculates the Buckingham exp-6 van der Waals energy using a pairwise neighbor list
EBUCK0D Subroutine
“ebuck0d” calculates the Buckingham exp-6 van der Waals energy via a Gaussian approximation
for potential energy smoothing
EBUCK1 Subroutine
“ebuck1” calculates the Buckingham exp-6 van der Waals energy and its first derivatives with re-
spect to Cartesian coordinates
EBUCK1A Subroutine
“ebuck1a” calculates the Buckingham exp-6 van der Waals energy and its first derivatives using a
pairwise double loop
EBUCK1B Subroutine
“ebuck1b” calculates the Buckingham exp-6 van der Waals energy and its first derivatives using the
method of lights
EBUCK1C Subroutine
“ebuck1c” calculates the Buckingham exp-6 van der Waals energy and its first derivatives using a
pairwise neighbor list
EBUCK1D Subroutine

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“ebuck1d” calculates the Buckingham exp-6 van der Waals energy and its first derivatives via a
Gaussian approximation for potential energy smoothing
EBUCK2 Subroutine
“ebuck2” calculates the Buckingham exp-6 van der Waals second derivatives for a single atom at a
time
EBUCK2A Subroutine
“ebuck2a” calculates the Buckingham exp-6 van der Waals second derivatives using a double loop
over relevant atom pairs
EBUCK2B Subroutine
“ebuck2b” calculates the Buckingham exp-6 van der Waals second derivatives via a Gaussian ap-
proximation for use with potential energy smoothing
EBUCK3 Subroutine
“ebuck3” calculates the Buckingham exp-6 van der Waals energy and partitions the energy among
the atoms
EBUCK3A Subroutine
“ebuck3a” calculates the Buckingham exp-6 van der Waals energy and partitions the energy among
the atoms using a pairwise double loop
EBUCK3B Subroutine
“ebuck3b” calculates the Buckingham exp-6 van der Waals energy and also partitions the energy
among the atoms using the method of lights
EBUCK3C Subroutine
“ebuck3c” calculates the Buckingham exp-6 van der Waals energy and also partitions the energy
among the atoms using a pairwise neighbor list
EBUCK3D Subroutine
“ebuck3d” calculates the Buckingham exp-6 van der Waals energy via a Gaussian approximation
for potential energy smoothing
ECHARGE Subroutine
“echarge” calculates the charge-charge interaction energy
ECHARGE0A Subroutine
“echarge0a” calculates the charge-charge interaction energy using a pairwise double loop
ECHARGE0B Subroutine
“echarge0b” calculates the charge-charge interaction energy using the method of lights
ECHARGE0C Subroutine
“echarge0c” calculates the charge-charge interaction energy using a pairwise neighbor list
ECHARGE0D Subroutine

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“echarge0d” calculates the charge-charge interaction energy using a particle mesh Ewald summa-
tion
ECHARGE0E Subroutine
“echarge0e” calculates the charge-charge interaction energy using a particle mesh Ewald summa-
tion and the method of lights
ECHARGE0F Subroutine
“echarge0f” calculates the charge-charge interaction energy using a particle mesh Ewald summa-
tion and a neighbor list
ECHARGE0G Subroutine
“echarge0g” calculates the charge-charge interaction energy for use with potential smoothing meth-
ods
ECHARGE1 Subroutine
“echarge1” calculates the charge-charge interaction energy and first derivatives with respect to
Cartesian coordinates
ECHARGE1A Subroutine
“echarge1a” calculates the charge-charge interaction energy and first derivatives with respect to
Cartesian coordinates using a pairwise double loop
ECHARGE1B Subroutine
“echarge1b” calculates the charge-charge interaction energy and first derivatives with respect to
Cartesian coordinates using the method of lights
ECHARGE1C Subroutine
“echarge1c” calculates the charge-charge interaction energy and first derivatives with respect to
Cartesian coordinates using a pairwise neighbor list
ECHARGE1D Subroutine
“echarge1d” calculates the charge-charge interaction energy and first derivatives with respect to
Cartesian coordinates using a particle mesh Ewald summation
ECHARGE1E Subroutine
“echarge1e” calculates the charge-charge interaction energy and first derivatives with respect to
Cartesian coordinates using a particle mesh Ewald summation and the method of lights
ECHARGE1F Subroutine
“echarge1f” calculates the charge-charge interaction energy and first derivatives with respect to
Cartesian coordinates using a particle mesh Ewald summation and a neighbor list
ECHARGE1G Subroutine
“echarge1g” calculates the charge-charge interaction energy and first derivatives with respect to
Cartesian coordinates for use with potential smoothing methods
ECHARGE2 Subroutine

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“echarge2” calculates second derivatives of the charge-charge interaction energy for a single atom
ECHARGE2A Subroutine
“echarge2a” calculates second derivatives of the charge-charge interaction energy for a single atom
using a pairwise loop
ECHARGE2B Subroutine
“echarge2b” calculates second derivatives of the charge-charge interaction energy for a single atom
using a neighbor list
ECHARGE2C Subroutine
“echarge2c” calculates second derivatives of the reciprocal space charge-charge interaction energy
for a single atom using a particle mesh Ewald summation via numerical differentiation
ECHARGE2D Subroutine
“echarge2d” calculates second derivatives of the real space charge-charge interaction energy for a
single atom using a pairwise loop
ECHARGE2E Subroutine
“echarge2e” calculates second derivatives of the real space charge-charge interaction energy for a
single atom using a pairwise neighbor list
ECHARGE2F Subroutine
“echarge2f” calculates second derivatives of the charge-charge interaction energy for a single atom
for use with potential smoothing methods
ECHARGE2R Subroutine
“echarge2r” computes reciprocal space charge-charge first derivatives; used to get finite difference
second derivatives
ECHARGE3 Subroutine
“echarge3” calculates the charge-charge interaction energy and partitions the energy among the
atoms
ECHARGE3A Subroutine
“echarge3a” calculates the charge-charge interaction energy and partitions the energy among the
atoms using a pairwise double loop
ECHARGE3B Subroutine
“echarge3b” calculates the charge-charge interaction energy and partitions the energy among the
atoms using the method of lights
ECHARGE3C Subroutine
“echarge3c” calculates the charge-charge interaction energy and partitions the energy among the
atoms using a pairwise neighbor list
ECHARGE3D Subroutine

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“echarge3d” calculates the charge-charge interaction energy and partitions the energy among the
atoms using a particle mesh Ewald summation
ECHARGE3E Subroutine
“echarge3e” calculates the charge-charge interaction energy and partitions the energy among the
atoms using a particle mesh Ewald summation and the method of lights
ECHARGE3F Subroutine
“echarge3f” calculates the charge-charge interaction energy and partitions the energy among the
atoms using a particle mesh Ewald summation and a pairwise neighbor list
ECHARGE3G Subroutine
“echarge3g” calculates the charge-charge interaction energy and partitions the energy among the
atoms for use with potential smoothing methods
ECHGDPL Subroutine
“echgdpl” calculates the charge-dipole interaction energy
ECHGDPL1 Subroutine
“echgdpl1” calculates the charge-dipole interaction energy and first derivatives with respect to
Cartesian coordinates
ECHGDPL2 Subroutine
“echgdpl2” calculates second derivatives of the charge-dipole interaction energy for a single atom
ECHGDPL3 Subroutine
“echgdpl3” calculates the charge-dipole interaction energy; also partitions the energy among the
atoms
ECHGTRN Subroutine
“echgtrn” calculates the charge transfer potential energy
ECHGTRN0A Subroutine
“echgtrn0a” calculates the charge transfer interaction energy using a double loop
ECHGTRN0B Subroutine
“echgtrn0b” calculates the charge transfer interaction energy using the method of lights
ECHGTRN0C Subroutine
“echgtrn0c” calculates the charge transfer interaction energy using a neighbor list
ECHGTRN1 Subroutine
“echgtrn1” calculates the charge transfer energy and first derivatives with respect to Cartesian
coordinates
ECHGTRN1A Subroutine
“echgtrn1a” calculates the charge transfer interaction energy and first derivatives using a double
loop

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ECHGTRN1B Subroutine
“echgtrn1b” calculates the charge transfer energy and first derivatives using a pairwise neighbor
list
ECHGTRN2 Subroutine
“echgtrn2” calculates the second derivatives of the charge transfer energy using a double loop over
relevant atom pairs
ECHGTRN3 Subroutine
“echgtrn3” calculates the charge transfer energy; also partitions the energy among the atoms
ECHGTRN3A Subroutine
“echgtrn3a” calculates the charge transfer interaction energy and also partitions the energy among
the atoms using a pairwise double loop
ECHGTRN3B Subroutine
“echgtrn3b” calculates the charge transfer interaction energy and also partitions the energy among
the atoms using the method of lights
ECHGTRN3C Subroutine
“echgtrn3c” calculates the charge transfer interaction energy and also partitions the energy among
the atoms using a pairwise neighbor list
ECRECIP Subroutine
“ecrecip” evaluates the reciprocal space portion of the particle mesh Ewald energy due to partial
charges
ECRECIP1 Subroutine
“ecrecip1” evaluates the reciprocal space portion of the particle mesh Ewald summation energy and
gradient due to partial charges
EDGE_ATTACH Subroutine
“edge_attach” checks if edge AB of a tetrahedron is “attached” to a given vertex C
EDGE_RADIUS Subroutine
“edge_radius” computes the radius of the smallest circumsphere to an edge, and compares it to
alpha
EDIFF Subroutine
“ediff” calculates the energy of polarizing the vacuum induced dipoles to their SCRF polarized
values
EDIFF1A Subroutine
“ediff1a” calculates the energy and derivatives of polarizing the vacuum induced dipoles to their
SCRF polarized values using a double loop
EDIFF1B Subroutine

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“ediff1b” calculates the energy and derivatives of polarizing the vacuum induced dipoles to their
SCRF polarized values using a neighbor list
EDIFF3 Subroutine
“ediff3” calculates the energy of polarizing the vacuum induced dipoles to their generalized Kirk-
wood values with energy analysis
EDIPOLE Subroutine
“edipole” calculates the dipole-dipole interaction energy
EDIPOLE1 Subroutine
“edipole1” calculates the dipole-dipole interaction energy and first derivatives with respect to Carte-
sian coordinates
EDIPOLE2 Subroutine
“edipole2” calculates second derivatives of the dipole-dipole interaction energy for a single atom
EDIPOLE3 Subroutine
“edipole3” calculates the dipole-dipole interaction energy; also partitions the energy among the
atoms
EDISP Subroutine
“edisp” calculates the damped dispersion potential energy
EDISP0A Subroutine
“edisp0a” calculates the damped dispersion potential energy using a pairwise double loop
EDISP0B Subroutine
“edisp0b” calculates the damped dispersion potential energy using a pairwise neighbor list
EDISP0C Subroutine
“edisp0c” calculates the dispersion interaction energy using particle mesh Ewald summation and a
double loop
EDISP0D Subroutine
“edisp0d” calculates the dispersion interaction energy using particle mesh Ewald summation and a
neighbor list
EDISP1 Subroutine
“edisp1” calculates the damped dispersion energy and first derivatives with respect to Cartesian
coordinates
EDISP1A Subroutine
“edisp1a” calculates the damped dispersion energy and derivatives with respect to Cartesian coor-
dinates using a pairwise double loop
EDISP1B Subroutine

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“edisp1b” calculates the damped dispersion energy and derivatives with respect to Cartesian coor-
dinates using a pairwise neighbor list
EDISP1C Subroutine
“edisp1c” calculates the damped dispersion energy and derivatives with respect to Cartesian coor-
dinates using particle mesh Ewald summation and a double loop
EDISP1D Subroutine
“edisp1d” calculates the damped dispersion energy and derivatives with respect to Cartesian coor-
dinates using particle mesh Ewald summation and a neighbor list
EDISP2 Subroutine
“edisp2” calculates the damped dispersion second derivatives for a single atom at a time
EDISP3 Subroutine
“edisp3” calculates the dispersion energy; also partitions the energy among the atoms
EDISP3A Subroutine
“edisp3a” calculates the dispersion potential energy and also partitions the energy among the atoms
using a pairwise double loop
EDISP3B Subroutine
“edisp3b” calculates the damped dispersion potential energy and also partitions the energy among
the atomsusing a pairwise neighbor list
EDISP3C Subroutine
“edisp3c” calculates the dispersion interaction energy using particle mesh Ewald summation and a
double loop
EDISP3D Subroutine
“edisp3d” calculates the damped dispersion energy and analysis using particle mesh Ewald sum-
mation and a neighbor list
EDREAL0C Subroutine
“edreal0c” calculates the damped dispersion potential energy using a particle mesh Ewald sum and
pairwise double loop
EDREAL0D Subroutine
“edreal0d” evaluated the real space portion of the damped dispersion energy using a neighbor list
EDREAL1C Subroutine
“edreal1c” evaluates the real space portion of the Ewald summation energy and gradient due to
damped dispersion interactions via a double loop
EDREAL1D Subroutine
“edreal1d” evaluates the real space portion of the Ewald summation energy and gradient due to
damped dispersion interactions via a neighbor list

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EDREAL3C Subroutine
“edreal3c” calculates the real space portion of the damped dispersion energy and analysis using
Ewald and a double loop
EDREAL3D Subroutine
“edreal3d” evaluated the real space portion of the damped dispersion energy and analysis using
Ewald and a neighbor list
EDRECIP Subroutine
“edrecip” evaluates the reciprocal space portion of the particle mesh Ewald energy due to damped
dispersion
EDRECIP1 Subroutine
“edrecip1” evaluates the reciprocal space portion of particle mesh Ewald energy and gradient due
to damped dispersion
EGAUSS Subroutine
“egauss” calculates the Gaussian expansion van der Waals energy
EGAUSS0A Subroutine
“egauss0a” calculates the Gaussian expansion van der Waals energy using a pairwise double loop
EGAUSS0B Subroutine
“egauss0b” calculates the Gaussian expansion van der Waals energy using the method of lights
EGAUSS0C Subroutine
“egauss0c” calculates the Gaussian expansion van der Waals energy using a pairwise neighbor list
EGAUSS0D Subroutine
“egauss0d” calculates the Gaussian expansion van der Waals energy for use with potential energy
smoothing
EGAUSS1 Subroutine
“egauss1” calculates the Gaussian expansion van der Waals interaction energy and its first deriva-
tives with respect to Cartesian coordinates
EGAUSS1A Subroutine
“egauss1a” calculates the Gaussian expansion van der Waals interaction energy and its first deriva-
tives using a pairwise double loop
EGAUSS1B Subroutine
“egauss1b” calculates the Gaussian expansion van der Waals energy and its first derivatives with
respect to Cartesian coordinates using the method of lights
EGAUSS1C Subroutine
“egauss1c” calculates the Gaussian expansion van der Waals energy and its first derivatives with
respect to Cartesian coordinates using a pairwise neighbor list

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EGAUSS1D Subroutine
“egauss1d” calculates the Gaussian expansion van der Waals interaction energy and its first deriva-
tives for use with potential energy smoothing
EGAUSS2 Subroutine
“egauss2” calculates the Gaussian expansion van der Waals second derivatives for a single atom at
a time
EGAUSS2A Subroutine
“egauss2a” calculates the Gaussian expansion van der Waals second derivatives using a pairwise
double loop
EGAUSS2B Subroutine
“egauss2b” calculates the Gaussian expansion van der Waals second derivatives for use with poten-
tial energy smoothing
EGAUSS3 Subroutine
“egauss3” calculates the Gaussian expansion van der Waals interaction energy and partitions the
energy among the atoms
EGAUSS3A Subroutine
“egauss3a” calculates the Gaussian expansion van der Waals energy and partitions the energy
among the atoms using a pairwise double loop
EGAUSS3B Subroutine
“egauss3b” calculates the Gaussian expansion van der Waals energy and partitions the energy
among the atoms using the method of lights
EGAUSS3C Subroutine
“egauss3c” calculates the Gaussian expansion van der Waals energy and partitions the energy
among the atoms using a pairwise neighbor list
EGAUSS3D Subroutine
“egauss3d” calculates the Gaussian expansion van der Waals interaction energy and partitions the
energy among the atoms for use with potential energy smoothing
EGB0A Subroutine
“egb0a” calculates the generalized Born polarization energy for the GB/SA solvation models using
a pairwise double loop
EGB0B Subroutine
“egb0b” calculates the generalized Born polarization energy for the GB/SA solvation models using
a pairwise neighbor list
EGB0C Subroutine
“egb0c” calculates the generalized Born polarization energy for the GB/SA solvation models for use
with potential smoothing methods via analogy to the smoothing of Coulomb’s law

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EGB1A Subroutine
“egb1a” calculates the generalized Born electrostatic energy and first derivatives of the GB/SA
solvation models using a double loop
EGB1B Subroutine
“egb1b” calculates the generalized Born electrostatic energy and first derivatives of the GB/SA
solvation models using a neighbor list
EGB1C Subroutine
“egb1c” calculates the generalized Born energy and first derivatives of the GB/SA solvation models
for use with potential smoothing methods
EGB2A Subroutine
“egb2a” calculates second derivatives of the generalized Born energy term for the GB/SA solvation
models
EGB2B Subroutine
“egb2b” calculates second derivatives of the generalized Born energy term for the GB/SA solvation
models for use with potential smoothing methods
EGB3A Subroutine
“egb3a” calculates the generalized Born electrostatic energy for GB/SA solvation models using a
pairwise double loop; also partitions the energy among the atoms
EGB3B Subroutine
“egb3b” calculates the generalized Born electrostatic energy for GB/SA solvation models using a
pairwise neighbor list; also partitions the energy among the atoms
EGB3C Subroutine
“egb3c” calculates the generalized Born electrostatic energy for GB/SA solvation models for use
with potential smoothing methods via analogy to the smoothing of Coulomb’s law; also partitions
the energy among the atoms
EGEOM Subroutine
“egeom” calculates the energy due to restraints on positions, distances, angles and torsions as well
as Gaussian basin and spherical droplet restraints
EGEOM1 Subroutine
“egeom1” calculates the energy and first derivatives with respect to Cartesian coordinates due
to restraints on positions, distances, angles and torsions as well as Gaussian basin and spherical
droplet restraints
EGEOM2 Subroutine
“egeom2” calculates second derivatives of restraints on positions, distances, angles and torsions as
well as Gaussian basin and spherical droplet restraints
EGEOM3 Subroutine

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“egeom3” calculates the energy due to restraints on positions, distances, angles and torsions as well
as Gaussian basin and droplet restraints; also partitions energy among the atoms
EGK Subroutine
“egk” calculates the generalized Kirkwood electrostatic solvation free energy for the GK/NP implicit
solvation model
EGK0A Subroutine
“egk0a” calculates the electrostatic portion of the implicit solvation energy via the generalized
Kirkwood model
EGK1 Subroutine
“egk1” calculates the implicit solvation energy and derivatives via the generalized Kirkwood plus
nonpolar implicit solvation
EGK1A Subroutine
“egk1a” calculates the electrostatic portion of the implicit solvation energy and derivatives via the
generalized Kirkwood model
EGK3 Subroutine
“egk3” calculates the generalized Kirkwood electrostatic energy for GK/NP solvation models; also
partitions the energy among the atoms
EGK3A Subroutine
“egk3a” calculates the electrostatic portion of the implicit solvation energy via the generalized
Kirkwood model; also partitions the energy among the atoms
EHAL Subroutine
“ehal” calculates the buffered 14-7 van der Waals energy
EHAL0A Subroutine
“ehal0a” calculates the buffered 14-7 van der Waals energy using a pairwise double loop
EHAL0B Subroutine
“ehal0b” calculates the buffered 14-7 van der Waals energy using the method of lights
EHAL0C Subroutine
“ehal0c” calculates the buffered 14-7 van der Waals energy using a pairwise neighbor list
EHAL1 Subroutine
“ehal1” calculates the buffered 14-7 van der Waals energy and its first derivatives with respect to
Cartesian coordinates
EHAL1A Subroutine
“ehal1a” calculates the buffered 14-7 van der Waals energy and its first derivatives with respect to
Cartesian coordinates using a pairwise double loop
EHAL1B Subroutine

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“ehal1b” calculates the buffered 14-7 van der Waals energy and its first derivatives with respect to
Cartesian coordinates using the method of lights
EHAL1C Subroutine
“ehal1c” calculates the buffered 14-7 van der Waals energy and its first derivatives with respect to
Cartesian coordinates using a pairwise neighbor list
EHAL2 Subroutine
“ehal2” calculates the buffered 14-7 van der Waals second derivatives for a single atom at a time
EHAL3 Subroutine
“ehal3” calculates the buffered 14-7 van der Waals energy and partitions the energy among the
atoms
EHAL3A Subroutine
“ehal3a” calculates the buffered 14-7 van der Waals energy and partitions the energy among the
atoms using a pairwise double loop
EHAL3B Subroutine
“ehal3b” calculates the buffered 14-7 van der Waals energy and also partitions the energy among
the atoms using the method of lights
EHAL3C Subroutine
“ehal3c” calculates the buffered 14-7 van der Waals energy and also partitions the energy among
the atoms using a pairwise neighbor list
EHPMF Subroutine
“ehpmf” calculates the hydrophobic potential of mean force energy using a pairwise double loop
EHPMF1 Subroutine
“ehpmf1” calculates the hydrophobic potential of mean force energy and first derivatives using a
pairwise double loop
EHPMF3 Subroutine
“ehpmf3” calculates the hydrophobic potential of mean force nonpolar energy; also partitions the
energy among the atoms
EIGEN Subroutine
“eigen” uses the power method to compute the largest eigenvalues and eigenvectors of the metric
matrix, “valid” is set true if the first three eigenvalues are positive
EIGENRGD Subroutine
EIGENROT Subroutine
EIGENROT Subroutine
EIGENTOR Subroutine
EIGENXYZ Subroutine

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EIMPROP Subroutine
“eimprop” calculates the improper dihedral potential energy
EIMPROP1 Subroutine
“eimprop1” calculates improper dihedral energy and its first derivatives with respect to Cartesian
coordinates
EIMPROP2 Subroutine
“eimprop2” calculates second derivatives of the improper dihedral angle energy for a single atom
EIMPROP3 Subroutine
“eimprop3” calculates the improper dihedral potential energy; also partitions the energy terms
among the atoms
EIMPTOR Subroutine
“eimptor” calculates the improper torsion potential energy
EIMPTOR1 Subroutine
“eimptor1” calculates improper torsion energy and its first derivatives with respect to Cartesian
coordinates
EIMPTOR2 Subroutine
“eimptor2” calculates second derivatives of the improper torsion energy for a single atom
EIMPTOR3 Subroutine
“eimptor3” calculates the improper torsion potential energy; also partitions the energy terms among
the atoms
ELJ Subroutine
“elj” calculates the Lennard-Jones 6-12 van der Waals energy
ELJ0A Subroutine
“elj0a” calculates the Lennard-Jones 6-12 van der Waals energy using a pairwise double loop
ELJ0B Subroutine
“elj0b” calculates the Lennard-Jones 6-12 van der Waals energy using the method of lights
ELJ0C Subroutine
“elj0c” calculates the Lennard-Jones 6-12 van der Waals energy using a pairwise neighbor list
ELJ0D Subroutine
“elj0d” calculates the Lennard-Jones 6-12 van der Waals energy via a Gaussian approximation for
potential energy smoothing
ELJ0E Subroutine
“elj0e” calculates the Lennard-Jones 6-12 van der Waals energy for use with stophat potential
energy smoothing

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ELJ1 Subroutine
“elj1” calculates the Lennard-Jones 6-12 van der Waals energy and its first derivatives with respect
to Cartesian coordinates
ELJ1A Subroutine
“elj1a” calculates the Lennard-Jones 6-12 van der Waals energy and its first derivatives using a
pairwise double loop
ELJ1B Subroutine
“elj1b” calculates the Lennard-Jones 6-12 van der Waals energy and its first derivatives using the
method of lights
ELJ1C Subroutine
“elj1c” calculates the Lennard-Jones 12-6 van der Waals energy and its first derivatives using a
pairwise neighbor list
ELJ1D Subroutine
“elj1d” calculates the Lennard-Jones 6-12 van der Waals energy
and its first derivatives via a Gaussian approximation for potential energy smoothing
ELJ1E Subroutine
“elj1e” calculates the van der Waals interaction energy and its first derivatives for use with stophat
potential energy smoothing
ELJ2 Subroutine
“elj2” calculates the Lennard-Jones 6-12 van der Waals second derivatives for a single atom at a
time
ELJ2A Subroutine
“elj2a” calculates the Lennard-Jones 6-12 van der Waals second derivatives using a double loop
over relevant atom pairs
ELJ2B Subroutine
“elj2b” calculates the Lennard-Jones 6-12 van der Waals second derivatives via a Gaussian approx-
imation for use with potential energy smoothing
ELJ2C Subroutine
“elj2c” calculates the Lennard-Jones 6-12 van der Waals second derivatives for use with stophat
potential energy smoothing
ELJ3 Subroutine
“elj3” calculates the Lennard-Jones 6-12 van der Waals energy and also partitions the energy among
the atoms
ELJ3A Subroutine
“elj3a” calculates the Lennard-Jones 6-12 van der Waals energy and also partitions the energy
among the atoms using a pairwise double loop

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ELJ3B Subroutine
“elj3b” calculates the Lennard-Jones 6-12 van der Waals energy and also partitions the energy
among the atoms using the method of lights
ELJ3C Subroutine
“elj3c” calculates the Lennard-Jones van der Waals energy and also partitions the energy among
the atoms using a pairwise neighbor list
ELJ3D Subroutine
“elj3d” calculates the Lennard-Jones 6-12 van der Waals energy and also partitions the energy
among the atoms via a Gaussian approximation for potential energy smoothing
ELJ3E Subroutine
“elj3e” calculates the Lennard-Jones 6-12 van der Waals energy and also partitions the energy
among the atoms for use with stophat potential energy smoothing
EMBED Subroutine
“embed” is a distance geometry routine patterned after the ideas of Gordon Crippen, Irwin Kuntz
and Tim Havel; it takes as input a set of upper and lower bounds on the interpoint distances,
chirality restraints and torsional restraints, and attempts to generate a set of coordinates that satisfy
the input bounds and restraints
EMETAL Subroutine
“emetal” calculates the transition metal ligand field energy
EMETAL1 Subroutine
“emetal1” calculates the transition metal ligand field energy and its first derivatives with respect to
Cartesian coordinates
EMETAL2 Subroutine
“emetal2” calculates the transition metal ligand field second derivatives for a single atom at a time
EMETAL3 Subroutine
“emetal3” calculates the transition metal ligand field energy and also partitions the energy among
the atoms
EMM3HB Subroutine
“emm3hb” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen bond-
ing energy
EMM3HB0A Subroutine
“emm3hb0a” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bonding energy using a pairwise double loop
EMM3HB0B Subroutine
“emm3hb0b” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bonding energy using the method of lights

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EMM3HB0C Subroutine
“emm3hb0c” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bonding energy using a pairwise neighbor list
EMM3HB1 Subroutine
“emm3hb1” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bonding energy with respect to Cartesian coordinates
EMM3HB1A Subroutine
“emm3hb1a” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bonding energy with respect to Cartesian coordinates using a pairwise double loop
EMM3HB1B Subroutine
“emm3hb1b” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bonding energy with respect to Cartesian coordinates using the method of lights
EMM3HB1C Subroutine
“emm3hb1c” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bonding energy with respect to Cartesian coordinates using a pairwise neighbor list
EMM3HB2 Subroutine
“emm3hb2” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bonding second derivatives for a single atom at a time
EMM3HB3 Subroutine
“emm3hb3” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bonding energy, and partitions the energy among the atoms
EMM3HB3A Subroutine
“emm3hb3” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bonding energy, and partitions the energy among the atoms
EMM3HB3B Subroutine
“emm3hb3b” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bonding energy using the method of lights
EMM3HB3C Subroutine
“emm3hb3c” calculates the MM3 exp-6 van der Waals and directional charge transfer hydrogen
bonding energy using a pairwise neighbor list
EMPOLE Subroutine
“empole” calculates the electrostatic energy due to atomic multipole interactions
EMPOLE0A Subroutine
“empole0a” calculates the atomic multipole interaction energy using a double loop
EMPOLE0B Subroutine

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“empole0b” calculates the atomic multipole interaction energy using a neighbor list
EMPOLE0C Subroutine
“empole0c” calculates the atomic multipole interaction energy using particle mesh Ewald summa-
tion and a double loop
EMPOLE0D Subroutine
“empole0d” calculates the atomic multipole interaction energy using particle mesh Ewald summa-
tion and a neighbor list
EMPOLE1 Subroutine
“empole1” calculates the atomic multipole energy and first derivatives with respect to Cartesian
coordinates
EMPOLE1A Subroutine
“empole1a” calculates the multipole energy and derivatives with respect to Cartesian coordinates
using a pairwise double loop
EMPOLE1B Subroutine
“empole1b” calculates the multipole energy and derivatives with respect to Cartesian coordinates
using a neighbor list
EMPOLE1C Subroutine
“empole1c” calculates the multipole energy and derivatives with respect to Cartesian coordinates
using particle mesh Ewald summation and a double loop
EMPOLE1D Subroutine
“empole1d” calculates the multipole energy and derivatives with respect to Cartesian coordinates
using particle mesh Ewald summation and a neighbor list
EMPOLE2 Subroutine
“empole2” calculates second derivatives of the multipole energy for a single atom at a time
EMPOLE2A Subroutine
“empole2a” computes multipole first derivatives for a single atom; used to get finite difference
second derivatives
EMPOLE3 Subroutine
“empole3” calculates the electrostatic energy due to atomic multipole interactions, and partitions
the energy among atoms
EMPOLE3A Subroutine
“empole3a” calculates the atomic multipole interaction energy using a double loop, and partitions
the energy among atoms
EMPOLE3B Subroutine
“empole3b” calculates the atomic multipole interaction energy using a neighbor list, and partitions
the energy among the atoms

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EMPOLE3C Subroutine
“empole3c” calculates the atomic multipole interaction energy using a particle mesh Ewald sum-
mation and double loop, and partitions the energy among the atoms
EMPOLE3D Subroutine
“empole3d” calculates the atomic multipole interaction energy using particle mesh Ewald summa-
tion and a neighbor list, and partitions the energy among the atoms
EMREAL0C Subroutine
“emreal0c” evaluates the real space portion of the Ewald sum energy due to atomic multipoles
using a double loop
EMREAL0D Subroutine
“emreal0d” evaluates the real space portion of the Ewald sum energy due to atomic multipoles
using a neighbor list
EMREAL1C Subroutine
“emreal1c” evaluates the real space portion of the Ewald summation energy and gradient due to
multipole interactions via a double loop
EMREAL1D Subroutine
“emreal1d” evaluates the real space portion of the Ewald summation energy and gradient due to
multipole interactions via a neighbor list
EMREAL3C Subroutine
“emreal3c” evaluates the real space portion of the Ewald sum energy due to atomic multipole
interactions and partitions the energy among the atoms
EMREAL3D Subroutine
“emreal3d” evaluates the real space portion of the Ewald sum energy due to atomic multipole
interactions, and partitions the energy among the atoms using a pairwise neighbor list
EMRECIP Subroutine
“emrecip” evaluates the reciprocal space portion of the particle mesh Ewald energy due to atomic
multipole interactions
EMRECIP1 Subroutine
“emrecip1” evaluates the reciprocal space portion of particle mesh Ewald summation energy and
gradient due to multipoles
ENERGY Function
“energy” calls the subroutines to calculate the potential energy terms and sums up to form the total
energy
ENP Subroutine
“enp” calculates the nonpolar implicit solvation energy as a sum of cavity and dispersion terms
ENP1 Subroutine

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“enp1” calculates the nonpolar implicit solvation energy and derivatives as a sum of cavity and
dispersion terms
ENP3 Subroutine
“enp3” calculates the nonpolar implicit solvation energy as a sum of cavity and dispersion terms;
also partitions the energy among the atoms
ENRGYZE Subroutine
“enrgyze” is an auxiliary routine for the analyze program that performs the energy analysis and
prints the total and intermolecular energies
EOPBEND Subroutine
“eopbend” computes the out-of-plane bend potential energy at trigonal centers via a Wilson-Decius-
Cross or Allinger angle
EOPBEND1 Subroutine
“eopbend1” computes the out-of-plane bend potential energy and first derivatives at trigonal cen-
ters via a Wilson-Decius-Cross or Allinger angle
EOPBEND2 Subroutine
“eopbend2” calculates second derivatives of the out-of-plane bend energy via a Wilson-Decius-Cross
or Allinger angle for a single atom using finite difference methods
EOPBEND2A Subroutine
“eopbend2a” calculates out-of-plane bend first derivatives at a trigonal center via a Wilson-Decius-
Cross or Allinger angle; used in computation of finite difference second derivatives
EOPBEND3 Subroutine
“eopbend3” computes the out-of-plane bend potential energy at trigonal centers via a Wilson-
Decius-Cross or Allinger angle; also partitions the energy among the atoms
EOPDIST Subroutine
“eopdist” computes the out-of-plane distance potential energy at trigonal centers via the central
atom height
EOPDIST1 Subroutine
“eopdist1” computes the out-of-plane distance potential energy and first derivatives at trigonal
centers via the central atom height
EOPDIST2 Subroutine
“eopdist2” calculates second derivatives of the out-of-plane distance energy for a single atom via
the central atom height
EOPDIST3 Subroutine
“eopdist3” computes the out-of-plane distance potential energy at trigonal centers via the central
atom height; also partitions the energy among the atoms
EPB Subroutine

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“epb” calculates the implicit solvation energy via the Poisson-Boltzmann plus nonpolar implicit
solvation
EPB1 Subroutine
“epb1” calculates the implicit solvation energy and derivatives via the Poisson-Boltzmann plus non-
polar implicit solvation
EPB1A Subroutine
“epb1a” calculates the solvation energy and gradients for the PB/NP solvation model
EPB3 Subroutine
“epb3” calculates the implicit solvation energy via the Poisson-Boltzmann model; also partitions
the energy among the atoms
EPITORS Subroutine
“epitors” calculates the pi-system torsion potential energy
EPITORS1 Subroutine
“epitors1” calculates the pi-system torsion potential energy and first derivatives with respect to
Cartesian coordinates
EPITORS2 Subroutine
“epitors2” calculates the second derivatives of the pi-system torsion energy for a single atom using
finite difference methods
EPITORS2A Subroutine
“epitors2a” calculates the pi-system torsion first derivatives; used in computation of finite difference
second derivatives
EPITORS3 Subroutine
“epitors3” calculates the pi-system torsion potential energy; also partitions the energy terms among
the atoms
EPOLAR Subroutine
“epolar” calculates the polarization energy due to induced dipole interactions
EPOLAR0A Subroutine
“epolar0a” calculates the induced dipole polarization energy using a double loop, and partitions
the energy among atoms
EPOLAR0B Subroutine
“epolar0b” calculates the induced dipole polarization energy using a neighbor list
EPOLAR0C Subroutine
“epolar0c” calculates the dipole polarization energy with respect to Cartesian coordinates using
particle mesh Ewald summation and a double loop
EPOLAR0D Subroutine

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“epolar0d” calculates the dipole polarization energy with respect to Cartesian coordinates using
particle mesh Ewald summation and a neighbor list
EPOLAR0E Subroutine
“epolar0e” calculates the dipole polarizability interaction from the induced dipoles times the elec-
tric field
EPOLAR1 Subroutine
“epolar1” calculates the induced dipole polarization energy and first derivatives with respect to
Cartesian coordinates
EPOLAR1A Subroutine
“epolar1a” calculates the dipole polarization energy and derivatives with respect to Cartesian coor-
dinates using a pairwise double loop
EPOLAR1B Subroutine
“epolar1b” calculates the dipole polarization energy and derivatives with respect to Cartesian coor-
dinates using a neighbor list
EPOLAR1C Subroutine
“epolar1c” calculates the dipole polarization energy and derivatives with respect to Cartesian coor-
dinates using particle mesh Ewald summation and a double loop
EPOLAR1D Subroutine
“epolar1d” calculates the dipole polarization energy and derivatives with respect to Cartesian coor-
dinates using particle mesh Ewald summation and a neighbor list
EPOLAR1E Subroutine
“epolar1e” calculates the dipole polarizability interaction from the induced dipoles times the elec-
tric field
EPOLAR2 Subroutine
“epolar2” calculates second derivatives of the dipole polarization energy for a single atom at a time
EPOLAR2A Subroutine
“epolar2a” computes polarization first derivatives for a single atom with respect to Cartesian coor-
dinates; used to get finite difference second derivatives
EPOLAR3 Subroutine
“epolar3” calculates the induced dipole polarization energy, and partitions the energy among atoms
EPOLAR3A Subroutine
“epolar3a” calculates the induced dipole polarization energy using a double loop, and partitions
the energy among atoms
EPOLAR3B Subroutine
“epolar3b” calculates the induced dipole polarization energy using a neighbor list, and partitions
the energy among atoms

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EPOLAR3C Subroutine
“epolar3c” calculates the polarization energy and analysis with respect to Cartesian coordinates
using particle mesh Ewald and a double loop
EPOLAR3D Subroutine
“epolar3d” calculates the polarization energy and analysis with respect to Cartesian coordinates
using particle mesh Ewald and a neighbor list
EPOLAR3E Subroutine
“epolar3e” calculates the dipole polarizability interaction from the induced dipoles times the elec-
tric field
EPREAL0C Subroutine
“epreal0c” calculates the induced dipole polarization energy using particle mesh Ewald summation
and a double loop
EPREAL0D Subroutine
“epreal0d” calculates the induced dipole polarization energy using particle mesh Ewald summation
and a neighbor list
EPREAL1C Subroutine
“epreal1c” evaluates the real space portion of the Ewald summation energy and gradient due to
dipole polarization via a double loop
EPREAL1D Subroutine
“epreal1d” evaluates the real space portion of the Ewald summation energy and gradient due to
dipole polarization via a neighbor list
EPREAL3C Subroutine
“epreal3c” calculates the induced dipole polarization energy and analysis using particle mesh Ewald
summation and a double loop
EPREAL3D Subroutine
“epreal3d” calculates the induced dipole polarization energy and analysis using particle mesh Ewald
and a neighbor list
EPRECIP Subroutine
“eprecip” evaluates the reciprocal space portion of particle mesh Ewald summation energy due to
dipole polarization
EPRECIP1 Subroutine
“eprecip1” evaluates the reciprocal space portion of the particle mesh Ewald summation energy
and gradient due to dipole polarization
EQUCLC Subroutine
EREPEL Subroutine
“erepel” calculates the Pauli exchange repulsion energy

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EREPEL0A Subroutine
“erepel0a” calculates the Pauli repulsion interaction energy using a double loop
EREPEL0B Subroutine
“erepel0b” calculates the Pauli repulsion interaction energy using a pairwise neighbor list
EREPEL1 Subroutine
“erepel1” calculates the Pauli repulsion energy and first derivatives with respect to Cartesian coor-
dinates
EREPEL1A Subroutine
“erepel1a” calculates the Pauli repulsion energy and first derivatives with respect to Cartesian co-
ordinates using a pairwise double loop
EREPEL1B Subroutine
“erepel1b” calculates the Pauli repulsion energy and first derivatives with respect to Cartesian co-
ordinates using a pariwise neighbor list
EREPEL2 Subroutine
“erepel2” calculates the second derivatives of the Pauli repulsion energy
EREPEL2A Subroutine
“erepel2a” computes Pauli repulsion first derivatives for a single atom via a double loop; used to
get finite difference second derivatives
EREPEL3 Subroutine
“erepel3” calculates the Pauli repulsion energy and partitions the energy among the atoms
EREPEL3A Subroutine
“erepel3a” calculates the Pauli repulsion energy and also partitions the energy among the atoms
using a double loop
EREPEL3B Subroutine
“erepel3b” calculates the Pauli repulsion energy and also partitions the energy among the atoms
using a neighbor list
ERF Function
“erf” computes a numerical approximation to the value of the error function via a Chebyshev ap-
proximation
ERFC Function
“erfc” computes a numerical approximation to the value of the complementary error function via a
Chebyshev approximation
ERFCORE Subroutine

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“erfcore” evaluates erf(x) or erfc(x) for a real argument x; when called with mode set to 0 it returns
erf, a mode of 1 returns erfc; uses rational functions that approximate erf(x) and erfc(x) to at least
18 significant decimal digits
ERFIK Subroutine
“erfik” compute the reaction field energy due to a single pair of atomic multipoles
ERFINV Function
“erfinv” evaluates the inverse of the error function for an argument in the range (-1,1) using a
rational function approximation followed by cycles of Newton-Raphson correction
ERXNFLD Subroutine
“erxnfld” calculates the macroscopic reaction field energy arising from a set of atomic multipoles
ERXNFLD1 Subroutine
“erxnfld1” calculates the macroscopic reaction field energy and derivatives with respect to Cartesian
coordinates
ERXNFLD2 Subroutine
“erxnfld2” calculates second derivatives of the macroscopic reaction field energy for a single atom
at a time
ERXNFLD3 Subroutine
“erxnfld3” calculates the macroscopic reaction field energy, and also partitions the energy among
the atoms
ESOLV Subroutine
“esolv” calculates the implicit solvation energy for surface area, generalized Born, generalized Kirk-
wood and Poisson-Boltzmann solvation models
ESOLV1 Subroutine
“esolv1” calculates the implicit solvation energy and first derivatives with respect to Cartesian coor-
dinates for surface area, generalized Born, generalized Kirkwood and Poisson-Boltzmann solvation
models
ESOLV2 Subroutine
“esolv2” calculates second derivatives of the implicit solvation energy for surface area, generalized
Born, generalized Kirkwood and Poisson-Boltzmann solvation models
ESOLV2A Subroutine
“esolv2a” calculates second derivatives of the implicit solvation potential energy by finite differ-
ences
ESOLV2B Subroutine
“esolv2b” finds implicit solvation gradients needed for calculation of the Hessian matrix by finite
differences
ESOLV3 Subroutine

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“esolv3” calculates the implicit solvation energy for surface area, generalized Born, generalized
Kirkwood and Poisson-Boltzmann solvation models; also partitions the energy among the atoms
ESTRBND Subroutine
“estrbnd” calculates the stretch-bend potential energy
ESTRBND1 Subroutine
“estrbnd1” calculates the stretch-bend potential energy and first derivatives with respect to Carte-
sian coordinates
ESTRBND2 Subroutine
“estrbnd2” calculates the stretch-bend potential energy second derivatives with respect to Cartesian
coordinates
ESTRBND3 Subroutine
“estrbnd3” calculates the stretch-bend potential energy; also partitions the energy among the atoms
ESTRTOR Subroutine
“estrtor” calculates the stretch-torsion potential energy
ESTRTOR1 Subroutine
“estrtor1” calculates the stretch-torsion energy and first derivatives with respect to Cartesian coor-
dinates
ESTRTOR2 Subroutine
“estrtor2” calculates the stretch-torsion potential energy second derivatives with respect to Carte-
sian coordinates
ESTRTOR3 Subroutine
“estrtor3” calculates the stretch-torsion potential energy; also partitions the energy terms among
the atoms
ETORS Subroutine
“etors” calculates the torsional potential energy
ETORS0A Subroutine
“etors0a” calculates the torsional potential energy using a standard sum of Fourier terms
ETORS0B Subroutine
“etors0b” calculates the torsional potential energy for use with potential energy smoothing methods
ETORS1 Subroutine
“etors1” calculates the torsional potential energy and first derivatives with respect to Cartesian
coordinates
ETORS1A Subroutine
“etors1a” calculates the torsional potential energy and first derivatives with respect to Cartesian
coordinates using a standard sum of Fourier terms

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ETORS1B Subroutine
“etors1b” calculates the torsional potential energy and first derivatives with respect to Cartesian
coordinates for use with potential energy smoothing methods
ETORS2 Subroutine
“etors2” calculates the second derivatives of the torsional energy for a single atom
ETORS2A Subroutine
“etors2a” calculates the second derivatives of the torsional energy for a single atom using a standard
sum of Fourier terms
ETORS2B Subroutine
“etors2b” calculates the second derivatives of the torsional energy for a single atom for use with
potential energy smoothing methods
ETORS3 Subroutine
“etors3” calculates the torsional potential energy; also partitions the energy among the atoms
ETORS3A Subroutine
“etors3a” calculates the torsional potential energy using a standard sum of Fourier terms and par-
titions the energy among the atoms
ETORS3B Subroutine
“etors3b” calculates the torsional potential energy for use with potential energy smoothing methods
and partitions the energy among the atoms
ETORTOR Subroutine
“etortor” calculates the torsion-torsion potential energy
ETORTOR1 Subroutine
“etortor1” calculates the torsion-torsion energy and first derivatives with respect to Cartesian coor-
dinates
ETORTOR2 Subroutine
“etortor2” calculates the torsion-torsion potential energy second derivatives with respect to Carte-
sian coordinates
ETORTOR3 Subroutine
“etortor3” calculates the torsion-torsion potential energy; also partitions the energy terms among
the atoms
EUREY Subroutine
“eurey” calculates the Urey-Bradley 1-3 interaction energy
EUREY1 Subroutine
“eurey1” calculates the Urey-Bradley interaction energy and its first derivatives with respect to
Cartesian coordinates

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EUREY2 Subroutine
“eurey2” calculates second derivatives of the Urey-Bradley interaction energy for a single atom at
a time
EUREY3 Subroutine
“eurey3” calculates the Urey-Bradley energy; also partitions the energy among the atoms
EVCORR Subroutine
“evcorr” computes the long range van der Waals correction to the energy via numerical integration
EVCORR1 Subroutine
“evcorr1” computes the long range van der Waals correction to the energy and virial via numerical
integration
EWALDCOF Subroutine
“ewaldcof” finds an Ewald coefficient such that all terms beyond the specified cutoff distance will
have a value less than a specified tolerance
EWCA Subroutine
“ewca” find the Weeks-Chandler-Andersen dispersion energy of a solute using an HCT-like method
EWCA1 Subroutine
“ewca1” finds the Weeks-Chandler-Anderson dispersion energy and derivatives of a solute
EWCA3 Subroutine
“ewca3” find the Weeks-Chandler-Andersen dispersion energy of a solute; also partitions the energy
among the atoms
EWCA3X Subroutine
“ewca3x” finds the Weeks-Chandler-Anderson dispersion energy of a solute using a numerical
“onion shell” method; also partitions the energy among the atoms
EWCAX Subroutine
“ewcax” finds the Weeks-Chandler-Anderson dispersion energy of a solute using a numerical “onion
shell” method
EXFIELD Subroutine
“exfield” calculates the electrostatic energy due to an external electric field applied to the system
EXFIELD1 Subroutine
“exfield1” calculates the electrostatic energy, gradient and virial due to an external electric field
applied to the system
EXFIELD3 Subroutine
“exfield3” calculates the electrostatic energy and partitions the energy among the atomsdue to an
external electric field applied to the system
EXPLORE Subroutine

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“explore” uses simulated annealing on an initial crude embedded distance geoemtry structure to
refine versus the bound, chirality, planarity and torsional error functions
EXTENT Subroutine
“extent” finds the largest interatomic distance in a system
EXTRA Subroutine
“extra” calculates any additional user defined potential energy contribution
EXTRA1 Subroutine
“extra1” calculates any additional user defined potential energy contribution and its first derivatives
EXTRA2 Subroutine
“extra2” calculates second derivatives of any additional user defined potential energy contribution
for a single atom at a time
EXTRA3 Subroutine
“extra3” calculates any additional user defined potential contribution and also partitions the energy
among the atoms
FATAL Subroutine
“fatal” terminates execution due to a user request, a severe error or some other nonstandard con-
dition
FFTBACK Subroutine
“fftback” performs a 3-D FFT backward transform via a single 3-D transform or three separate 1-D
transforms
FFTCLOSE Subroutine
“fftclose” does cleanup after performing a 3-D FFT by destroying the FFTW plans for the forward
and backward transforms
FFTFRONT Subroutine
“fftfront” performs a 3-D FFT forward transform via a single 3-D transform or three separate 1-D
transforms
FFTSETUP Subroutine
“fftsetup” does initialization for a 3-D FFT to be computed via either the FFTPACK or FFTW libraries
FIELD Subroutine
“field” sets the force field potential energy functions from a parameter file and modifications speci-
fied in a keyfile
FINAL Subroutine
“final” performs any final program actions such as deallocation of global memory, prints a status
message, and then pauses if necessary to avoid closing the execution window
FINDATM Subroutine

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“findatm” locates a specific PDB atom name type within a range of atoms from the PDB file, returns
zero if the name type was not found
FINDNUC Subroutine
“findnuc” locates and stores the atoms in nucleotide units based on atomic element and connectivity
information
FINDPRO Subroutine
“findpro” locates and stores the atoms in amino acid residues based on atomic element and con-
nectivity information
FINDSEQ Subroutine
“findseq” locates and stores biopolymer sequences for proteins and nucleic acids from connectivity
and residue information
FITRSD Subroutine
“fitrsd” computes residuals for electrostatic potential fitting including total charge restraints, dipole
and quadrupole moment targets, and restraints to initial parameter values
FITTORS Subroutine
“fittors” refines torsion parameters based on a quantum mechanical optimized energy surface
FIXFRAME Subroutine
“fixframe” is a service routine that alters the local frame definition for specified atoms
FIXPDB Subroutine
“fixpdb” corrects problems with PDB files by converting residue and atom names to the standard
forms used by Tinker
FIXPOLE Subroutine
“fixpole” performs unit conversion of the multipole components, rounds moments to desired preci-
sion, and enforces integer net charge and traceless quadrupoles
FLATTEN Subroutine
“flatten” sets the type of smoothing method and the extent of surface deformation for use with
potential energy smoothing
FLIPJW Subroutine
“flipjw” goes over the linkfacet list to restore regularity after a point has been inserted; when a
linkfacet is found nonregular and flippable, attempt to flip it; if the flip is successful, new linkfacets
are added to the queue; terminate when the linkfacet list is empty
FPHI_MPOLE Subroutine
“fphi_mpole” extracts the permanent multipole potential from the particle mesh Ewald grid
FPHI_TO_CPHI Subroutine
“fphi_to_cphi” transforms the reciprocal space potential from fractional to Cartesian coordinates

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FPHI_UIND Subroutine
“fphi_uind” extracts the induced dipole potential from the particle mesh Ewald grid
FRACDIST Subroutine
“fracdist” computes a normalized distribution of the pairwise fractional distances between the
smoothed upper and lower bounds
FRAC_TO_CART Subroutine
“frac_to_cart” computes a transformation matrix to convert a multipole object in fraction coordi-
nates to Cartesian
FRAME13 Subroutine
“frame13” finds local coordinate frame defining atoms in cases where the use of 1-3 connected
atoms is required
FREEUNIT Function
“freeunit” finds an unopened Fortran I/O unit and returns its numerical value from 1 to 99; the
units already assigned to “input” and “iout” (usually 5 and 6) are skipped since they have special
meaning as the default I/O units
GAMMLN Function
“gammln” uses a series expansion due to Lanczos to compute the natural logarithm of the Gamma
function at “x” in [0,1]
GAUSSJORDAN Subroutine
“gaussjordan” solves a system of linear equations by using the method of Gaussian elimination with
partial pivoting
GDA Program
“gda” implements Gaussian Density Annealing (GDA) algorithm for global optimization via simu-
lated annealing
GDA1 Subroutine
GDA2 Function
GDA3 Subroutine
GDASTAT Subroutine
for a GDA integration step; also saves the coordinates
GENDOT Subroutine
“gendot” finds the coordinates of a specified number of surface points for a sphere with the input
radius and coordinate center
GEODESIC Subroutine
“geodesic” smooths the upper and lower distance bounds via the triangle inequality using a sparse
matrix version of a shortest path algorithm

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GEOMETRY Function
“geometry” finds the value of the interatomic distance, angle or dihedral angle defined by two to
four input atoms
GETARC Subroutine
“getarc” asks for a coordinate archive or trajectory file name, then reads the formatted or binary
archive file
GETBASE Subroutine
“getbase” finds the base heavy atoms for a single nucleotide residue and copies the names and
coordinates to the Protein Data Bank file
GETCART Subroutine
“getcart” asks for a Cartesian coordinate file name, then reads the formatted or binary coordinates
file
GETCHUNK Subroutine
“getchunk” determines the number of grid point “chunks” used along each axis of the PME grid for
parallelization
GETDCD Subroutine
“getdcd” asks for a binary DCD trajectory file name and the corresponding Tinker coordinates file,
then reads the initial set of DCD coordinates
GETINT Subroutine
“getint” asks for an internal coordinate file name, then reads the internal coordinates and computes
Cartesian coordinates
GETKEY Subroutine
“getkey” finds a valid keyfile and stores its contents as line images for subsequent keyword param-
eter searching
GETMOL Subroutine
“getmol” asks for a MDL MOL molecule file name, then reads the coordinates from the file
GETMOL2 Subroutine
“getmol2” asks for a Tripos MOL2 molecule file name, then reads the coordinates from the file
GETMONITOR Subroutine
GETNUCH Subroutine
“getnuch” finds the nucleotide hydrogen atoms for a single residue and copies the names and
coordinates to the Protein Data Bank file
GETNUMB Subroutine
“getnumb” searches an input string from left to right for an integer and puts the numeric value in
“number”; returns zero with “next” unchanged if no integer value is found

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GETPDB Subroutine
“getpdb” asks for a Protein Data Bank file name, then reads in the coordinates file
GETPRB Subroutine
“getprb” tests for a possible probe position at the interface between three neighboring atoms
GETPRM Subroutine
“getprm” finds the potential energy parameter file and then opens and reads the parameters
GETPROH Subroutine
“getproh” finds the hydrogen atoms for a single amino acid residue and copies the names and
coordinates to the Protein Data Bank file
GETREF Subroutine
“getref” copies structure information from the reference area into the standard variables for the
current system structure
GETSEQ Subroutine
“getseq” asks the user for the amino acid sequence and torsional angle values needed to define a
peptide
GETSEQN Subroutine
“getseqn” asks the user for the nucleotide sequence and torsional angle values needed to define a
nucleic acid
GETSIDE Subroutine
“getside” finds the side chain heavy atoms for a single amino acid residue and copies the names
and coordinates to the Protein Data Bank file
GETSTRING Subroutine
“getstring” searches for a quoted text string within an input character string; the region between
the first and second double quote is returned as the “text”; if the actual text is too long, only the
first part is returned
GETTEXT Subroutine
“gettext” searches an input string for the first string of non-blank characters; the region from a
non-blank character to the first space or tab is returned as “text”; if the actual text is too long, only
the first part is returned
GETTIME Subroutine
“gettime” finds the elapsed wall clock and CPU times in seconds since the last call to “settime”
GETTOR Subroutine
“gettor” tests for a possible torus position at the interface between two atoms, and finds the torus
radius, center and axis
GETWORD Subroutine

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“getword” searches an input string for the first alphabetic character (A-Z or a-z); the region from
this first character to the first blank space or separator is returned as a “word”; if the actual word
is too long, only the first part is returned
GETXYZ Subroutine
“getxyz” asks for a Cartesian coordinate file name, then reads in the coordinates file
GHMCSTEP Subroutine
“ghmcstep” performs a single stochastic dynamics time step via the generalized hybrid Monte Carlo
(GHMC) algorithm to ensure exact sampling from the Boltzmann density
GHMCTERM Subroutine
“ghmcterm” finds the friction and fluctuation terms needed to update velocities during GHMC
stochastic dynamics
GRADFAST Subroutine
“gradfast” calculates the potential energy and first derivatives for the fast-evolving local valence
potential energy terms
GRADIENT Subroutine
“gradient” calls subroutines to calculate the potential energy and first derivatives with respect to
Cartesian coordinates
GRADRGD Subroutine
“gradrgd” calls subroutines to calculate the potential energy and first derivatives with respect to
rigid body coordinates
GRADROT Subroutine
“gradrot” calls subroutines to calculate the potential energy and its torsional first derivatives
GRADSLOW Subroutine
“gradslow” calculates the potential energy and first derivatives for the slow-evolving nonbonded
potential energy terms
GRAFIC Subroutine
“grafic” outputs the upper & lower triangles and diagonal of a square matrix in a schematic form
for visual inspection
GRID_DISP Subroutine
“grid_disp” places the damped dispersion coefficients onto the particle mesh Ewald grid
GRID_MPOLE Subroutine
“grid_mpole” places the fractional atomic multipoles onto the particle mesh Ewald grid
GRID_PCHG Subroutine
“grid_pchg” places the fractional atomic partial charges onto the particle mesh Ewald grid
GRID_UIND Subroutine

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“grid_uind” places the fractional induced dipoles onto the particle mesh Ewald grid
GROUPS Subroutine
“groups” tests a set of atoms to see if all are members of a single atom group or a pair of atom
groups; if so, then the correct intra- or intergroup weight is assigned
GRPLINE Subroutine
“grpline” tests each atom group for linearity of the sites contained in the group
GSORT Subroutine
“gsort” uses the Gram-Schmidt algorithm to build orthogonal vectors for sliding block interative
matrix diagonalization
GYRATE Subroutine
“gyrate” computes the radius of gyration of a molecular system from its atomic coordinates; only
active atoms are included
HANGLE Subroutine
“hangle” constructs hybrid angle bending parameters given an initial state, final state and “lambda”
value
HATOM Subroutine
“hatom” assigns a new atom type to each hybrid site
HBOND Subroutine
“hbond” constructs hybrid bond stretch parameters given an initial state, final state and “lambda”
value
HCHARGE Subroutine
“hcharge” constructs hybrid charge interaction parameters given an initial state, final state and
“lambda” value
HDIPOLE Subroutine
“hdipole” constructs hybrid dipole interaction parameters given an initial state, final state and
“lambda” value
HESSBLK Subroutine
“hessblk” calls subroutines to calculate the Hessian elements for each atom in turn with respect to
Cartesian coordinates
HESSIAN Subroutine
“hessian” calls subroutines to calculate the Hessian elements for each atom in turn with respect to
Cartesian coordinates
HESSRGD Subroutine
“hessrgd” computes the numerical Hessian elements with respect to rigid body coordinates via
6*ngroup+1 gradient evaluations

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HESSROT Subroutine
“hessrot” computes numerical Hessian elements with respect to torsional angles; either the diagonal
or the full matrix can be calculated; the full matrix needs nomega+1 gradient evaluations while
the diagonal needs just two evaluations
HETATOM Subroutine
“hetatom” translates water molecules and ions in Protein Data Bank format to a Cartesian coordi-
nate file and sequence file
HIMPTOR Subroutine
“himptor” constructs hybrid improper torsional parameters given an initial state, final state and
“lambda” value
HOOVER Subroutine
“hoover” applies a combined thermostat and barostat via a Nose-Hoover chain algorithm
HSTRBND Subroutine
“hstrbnd” constructs hybrid stretch-bend parameters given an initial state, final state and “lambda”
value
HSTRTOR Subroutine
“hstrtor” constructs hybrid stretch-torsion parameters given an initial state, final state and “lambda”
value
HTORS Subroutine
“htors” constructs hybrid torsional parameters for a given initial state, final state and “lambda”
value
HVDW Subroutine
“hvdw” constructs hybrid van der Waals parameters given an initial state, final state and “lambda”
value
HYBRID Subroutine
“hybrid” constructs the hybrid hamiltonian for a specified initial state, final state and mutation
parameter “lambda”
IJKPTS Subroutine
“ijkpts” stores a set of indices used during calculation of macroscopic reaction field energetics
IMAGE Subroutine
“image” takes the components of pairwise distance between two points in a periodic box and con-
verts to the components of the minimum image distance
IMAGEN Subroutine
“imagen” takes the components of pairwise distance between two points and converts to the com-
ponents of the minimum image distance
IMAGER Subroutine

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“imager” takes the components of pairwise distance between two points in the same or neighboring
periodic boxes and converts to the components of the minimum image distance
IMPOSE Subroutine
“impose” performs the least squares best superposition of two atomic coordinate sets via a quater-
nion method; upon return, the first coordinate set is unchanged while the second set is translated
and rotated to give best fit; the final root mean square fit is returned in “rmsvalue”
INDTCGA Subroutine
“indtcga” computes the induced dipoles and intermediates used in polarization force calculation
for the TCG method with dp cross terms = true, initial guess mu0 = 0 and using a diagonal
preconditioner
INDTCGB Subroutine
“indtcgb” computes the induced dipoles and intermediates used in polarization force calculation
for the TCG method with dp cross terms = true, initial guess mu0 = direct and using diagonal
preconditioner
INDUCE Subroutine
“induce” computes the induced dipole moments at polarizable sites due to direct or mutual polar-
ization
INDUCE0A Subroutine
“induce0a” computes the induced dipole moments at polarizable sites using a preconditioned con-
jugate gradient solver
INDUCE0B Subroutine
“induce0b” computes and stores the induced dipoles via the truncated conjugate gradient (TCG)
method
INDUCE0C Subroutine
“induce0c” computes the induced dipole moments at polarizable sites for generalized Kirkwood
SCRF and vacuum environments
INDUCE0D Subroutine
“induce0d” computes the induced dipole moments at polarizable sites for Poisson-Boltzmann SCRF
and vacuum environments
INEDGE Subroutine
“inedge” inserts a concave edge into the linked list for its temporary torus
INERTIA Subroutine
“inertia” computes the principal moments of inertia for the system, and optionally translates the
center of mass to the origin and rotates the principal axes onto the global axes
INITATOM Subroutine
“initatom” sets the atomic symbol, standard atomic weight, van der Waals radius and covalent
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INITERR Function
“initerr” is the initial error function and derivatives for a distance geometry embedding; it includes
components from the local geometry and torsional restraint errors
INITIAL Subroutine
“initial” sets up original values for some parameters and variables that might not otherwise get
initialized
INITMMFF Subroutine
“initmmff” initializes some parameter values for the Merck Molecular force field
INITPRM Subroutine
“initprm” completely initializes a force field by setting all parameters to zero and using defaults for
control values
INITRES Subroutine
“initres” sets biopolymer residue names and biotype codes used in PDB file conversion and auto-
mated generation of structures
INITROT Subroutine
“initrot” sets the torsional angles which are to be rotated in subsequent computation, by default
automatically selects all rotatable single bonds; optionally makes atoms inactive when they are not
moved by any torsional rotation
INSERT Subroutine
“insert” adds the specified atom to the Cartesian coordinates list and shifts the remaining atoms
INSIDE_TETRA_JW Subroutine
“inside_tetra_jw” tests if a point P is inside the tetrahedron defined by four points ABCD with
orientation “iorient”, if P is inside the tetrahedron, then also checks if it is redundant
INTEDIT Program
“intedit” allows the user to extract information from or alter the values within an internal coordi-
nates file
INTERPOL Subroutine
“interpol” computes intergroup induced dipole moments for use during removal of intergroup po-
larization
INTXYZ Program
“intxyz” takes as input an internal coordinates file, converts to and then writes out Cartesian coor-
dinates
INVBETA Function
“invbeta” computes the inverse Beta distribution function via a combination of Newton iteration
and bisection search
INVERT Subroutine

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“invert” inverts a matrix using the Gauss-Jordan method

IPEDGE Subroutine
“ipedge” inserts convex edge into linked list for atom
JACOBI Subroutine
“jacobi” performs a matrix diagonalization of a real symmetric matrix by the method of Jacobi
rotations
JUSTIFY Subroutine
“justify” converts a text string to right justified format with leading blank spaces
KANGANG Subroutine
“kangang” assigns the parameters for angle-angle cross term interactions and processes new or
changed parameter values
KANGLE Subroutine
“kangle” assigns the force constants and ideal angles for the bond angles; also processes new or
changed parameters
KANGLEM Subroutine
“kanglem” assigns the force constants and ideal angles for bond angles according to the Merck
Molecular Force Field (MMFF)
KANGTOR Subroutine
“kangtor” assigns parameters for angle-torsion interactions and processes new or changed parame-
ter values
KATOM Subroutine
“katom” assigns an atom type definitions to each atom in the structure and processes any new or
changed values
KBOND Subroutine
“kbond” assigns a force constant and ideal bond length to each bond in the structure and processes
any new or changed parameter values
KBONDM Subroutine
“kbondm” assigns a force constant and ideal bond length to each bond according to the Merck
Molecular Force Field (MMFF)
KCHARGE Subroutine
“kcharge” assigns partial charges to the atoms within the structure and processes any new or
changed values
KCHARGEM Subroutine
“kchargem” assigns partial charges to the atoms according to the Merck Molecular Force Field
(MMFF)

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KCHGFLX Subroutine
“kchgflx” assigns a force constant and ideal bond length to each bond in the structure and processes
any new or changed parameter values
KCHGTRN Subroutine
“kchgtrn” assigns charge magnitude and damping parameters for charge transfer interactions and
processes any new or changed values for these parameters
KCHIRAL Subroutine
“kchiral” determines the target value for each chirality and planarity restraint as the signed volume
of the parallelpiped spanned by vectors from a common atom to each of three other atoms
KDIPOLE Subroutine
“kdipole” assigns bond dipoles to the bonds within the structure and processes any new or changed
values
KDISP Subroutine
“kdisp” assigns C6 coefficients and damping parameters for dispersion interactions and processes
any new or changed values for these parameters
KENEG Subroutine
“keneg” applies primary and secondary electronegativity bond length corrections to applicable bond
parameters
KEWALD Subroutine
“kewald” assigns particle mesh Ewald parameters and options for a periodic system
KEXTRA Subroutine
“kextra” assigns parameters to any additional user defined potential energy contribution
KGB Subroutine
“kgb” initializes parameters needed for the generalized Born implicit solvation models
KGEOM Subroutine
“kgeom” asisgns parameters for geometric restraint terms to be included in the potential energy
calculation
KGK Subroutine
“kgk” initializes parameters needed for the generalized Kirkwood implicit solvation model
KHPMF Subroutine
“khpmf” initializes parameters needed for the hydrophobic potential of mean force nonpolar im-
plicit solvation model
KIMPROP Subroutine
“kimprop” assigns potential parameters to each improper dihedral in the structure and processes
any changed values

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KIMPTOR Subroutine
“kimptor” assigns torsional parameters to each improper torsion in the structure and processes any
changed values
KINAUX Subroutine
“kinaux” computes the total kinetic energy and temperature for auxiliary dipole variables used in
iEL polarization
KINETIC Subroutine
“kinetic” computes the total kinetic energy and kinetic energy contributions to the pressure tensor
by summing over velocities
KMETAL Subroutine
“kmetal” assigns ligand field parameters to transition metal atoms and processes any new or
changed parameter values
KMPOLE Subroutine
“kmpole” assigns atomic multipole moments to the atoms of the structure and processes any new
or changed values
KNP Subroutine
“knp” initializes parameters needed for the cavity-plus- dispersion nonpolar implicit solvation
model
KONVEC Subroutine
“konvec” finds a Hessian-vector product via finite-difference evaluation of the gradient based on
atomic displacements
KOPBEND Subroutine
“kopbend” assigns the force constants for out-of-plane bends at trigonal centers via Wilson-Decius-
Cross or Allinger angles; also processes any new or changed parameter values
KOPBENDM Subroutine
“kopbendm” assigns the force constants for out-of-plane bends according to the Merck Molecular
Force Field (MMFF)
KOPDIST Subroutine
“kopdist” assigns the force constants for out-of-plane distance at trigonal centers via the central
atom height; also processes any new or changed parameter values
KORBIT Subroutine
“korbit” assigns pi-orbital parameters to conjugated systems and processes any new or changed
parameters
KPB Subroutine
“kpb” assigns parameters needed for the Poisson-Boltzmann implicit solvation model implemented
via APBS

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KPITORS Subroutine
“kpitors” assigns pi-system torsion parameters to torsions needing them, and processes any new or
changed values
KPOLAR Subroutine
“kpolar” assigns atomic dipole polarizabilities to the atoms within the structure and processes any
new or changed values
KREPEL Subroutine
“krepel” assigns the size values, exponential parameter and number of valence electrons for Pauli
repulsion interactions and processes any new or changed values for these parameters
KSA Subroutine
“ksa” initializes parameters needed for surface area-based implicit solvation models including ASP
and SASA
KSOLV Subroutine
“ksolv” assigns implicit solvation energy parameters for the surface area, generalized Born, gener-
alized Kirkwood, Poisson-Boltzmann, cavity-dispersion and HPMF models
KSTRBND Subroutine
“kstrbnd” assigns parameters for stretch-bend interactions and processes new or changed parameter
values
KSTRBNDM Subroutine
“kstrbndm” assigns parameters for stretch-bend interactions according to the Merck Molecular
Force Field (MMFF)
KSTRTOR Subroutine
“kstrtor” assigns stretch-torsion parameters to torsions needing them, and processes any new or
changed values
KSURF Subroutine
“ksurf” reads control values used within the AlphaMol code for determination of molecular surface
area and volume
KTORS Subroutine
“ktors” assigns torsional parameters to each torsion in the structure and processes any new or
changed values
KTORSM Subroutine
“ktorsm” assigns torsional parameters to each torsion according to the Merck Molecular Force Field
(MMFF)
KTORTOR Subroutine
“ktortor” assigns torsion-torsion parameters to adjacent torsion pairs and processes any new or
changed values

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KUNDROT1 Subroutine
“kundrot1” calculates first derivatives of the total excluded volume with respect to the Cartesian
coordinates of each atom using a numerical method due to Craig Kundrot
KUNDROT2 Subroutine
“kundrot2” calculates second derivatives of the total excluded volume with respect to the Cartesian
coordinates of the atoms using a numerical method due to Craig Kundrot
KUREY Subroutine
“kurey” assigns the force constants and ideal distances for the Urey-Bradley 1-3 interactions; also
processes any new or changed parameter values
KVDW Subroutine
“kvdw” assigns the parameters to be used in computing the van der Waals interactions and pro-
cesses any new or changed values for these parameters
LATTICE Subroutine
“lattice” stores the periodic box dimensions and sets angle values to be used in computing fractional
coordinates
LBFGS Subroutine
“lbfgs” is a limited memory BFGS quasi-newton nonlinear optimization routine
LIGASE Subroutine
“ligase” translates a nucleic acid structure in Protein Data Bank format to a Cartesian coordinate
file and sequence file
LIGHTS Subroutine
“lights” computes the set of nearest neighbor interactions using the method of lights algorithm
LINBODY Subroutine
“linbody” finds the angular velocity of a linear rigid body given the inertia tensor and angular
momentum
LMSTEP Subroutine
“lmstep” computes a Levenberg-Marquardt step during a nonlinear least squares calculation using
ideas from the MINPACK LMPAR routine and the internal doubling strategy of Dennis and Schnabel
LOCALMIN Subroutine
“localmin” is used during normal mode local search to perform a Cartesian coordinate energy
minimization
LOCALRGD Subroutine
“localrgd” is used during the PSS local search procedure to perform a rigid body energy minimiza-
tion
LOCALROT Subroutine

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“localrot” is used during the PSS local search procedure to perform a torsional space energy mini-
mization
LOCALXYZ Subroutine
“localxyz” is used during the potential smoothing and search procedure to perform a local opti-
mization at the current smoothing level
LOCATE_JW Subroutine
“locate_jw” finds the tetrahedron containing a new point to be added in the triangulation
LOCERR Function
“locerr” is the local geometry error function and derivatives including the 1-2, 1-3 and 1-4 distance
bound restraints
LOWCASE Subroutine
“lowcase” converts a text string to all lower case letters
MAJORIZE Subroutine
“majorize” refines the projected coordinates by attempting to minimize the least square residual
between the trial distance matrix and the distances computed from the coordinates
MAKEBAR Subroutine
MAKEBOX Subroutine
“makebox” builds a periodic box of a desired size by randomly copying a specified number of
monomers into a target box size, followed by optional excluded volume refinement
MAKEINT Subroutine
“makeint” converts Cartesian to internal coordinates where selection of internal coordinates is con-
trolled by “mode”
MAKEPDB Subroutine
“makepdb” cconstructs a Protein Data Bank file from a set of Cartesian coordinates with special
handling for systems consisting of biopolymer chains, ligands and water molecules
MAKEREF Subroutine
“makeref” copies the information contained in the “xyz” file of the current structure into corre-
sponding reference areas
MAKEXYZ Subroutine
“makexyz” generates a complete set of Cartesian coordinates for a full structure from the internal
coordinate values
MAPCHECK Subroutine
“mapcheck” checks the current minimum energy structure for possible addition to the master list
of local minima
MATCH1 Subroutine

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“match1” finds and stores the first multipole component found on a line of output from Stone’s
GDMA program
MATCH2 Subroutine
“match2” finds and stores the second multipole component found on a line of output from Stone’s
GDMA program
MATCH3 Subroutine
“match3” finds and stores the third multipole component found on a line of output from Stone’s
GDMA program
MAXWELL Function
“maxwell” returns a speed in Angstroms/picosecond randomly selected from a 3-D Maxwell-
Boltzmann distribution for the specified particle mass and system temperature
MBUILD Subroutine
“mbuild” performs a complete rebuild of the atomic multipole electrostatic neighbor list for all sites
MCM1 Function
“mcm1” is a service routine that computes the energy and gradient for truncated Newton optimiza-
tion in Cartesian coordinate space
MCM2 Subroutine
“mcm2” is a service routine that computes the sparse matrix Hessian elements for truncated Newton
optimization in Cartesian coordinate space
MCMSTEP Function
“mcmstep” implements the minimization phase of an MCM step via Cartesian minimization follow-
ing a Monte Carlo step
MDINIT Subroutine
“mdinit” initializes the velocities and accelerations for a molecular dynamics trajectory, including
restarts
MDREST Subroutine
“mdrest” finds and removes any translational or rotational kinetic energy of the center of mass of
the overall system, of rigid bodies or of user-defined atom groups
MDSAVE Subroutine
“mdsave” writes molecular dynamics trajectory snapshots and auxiliary files with velocity, force or
induced dipole data; also checks for user requested termination of a simulation
MDSTAT Subroutine
“mdstat” is called at each molecular dynamics time step to form statistics on various average values
and fluctuations, and to periodically save the state of the trajectory
MEASFN Subroutine
MEASFQ Subroutine

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MEASFS Subroutine
MEASPM Subroutine
“measpm” computes the volume of a single prism section of the full interior polyhedron
MECHANIC Subroutine
“mechanic” sets up needed parameters for the potential energy calculation and reads in many of
the user selectable options
MERGE Subroutine
“merge” combines the reference and current structures into a single new “current” structure con-
taining the reference atoms followed by the atoms of the current structure
METRIC Subroutine
“metric” takes as input the trial distance matrix and computes the metric matrix of all possible
dot products between the atomic vectors and the center of mass using the law of cosines and the
following formula for the distances to the center of mass:
MIDERR Function
“miderr” is the secondary error function and derivatives for a distance geometry embedding; it
includes components from the distance bounds, local geometry, chirality and torsional restraint
errors
MINIMIZ1 Function
“minimiz1” is a service routine that computes the energy and gradient for a low storage BFGS
optimization in Cartesian coordinate space
MINIMIZE Program
“minimize” performs energy minimization in Cartesian coordinate space using a low storage BFGS
nonlinear optimization
MINIROT Program
“minirot” performs an energy minimization in torsional angle space using a low storage BFGS
nonlinear optimization
MINIROT1 Function
“minirot1” is a service routine that computes the energy and gradient for a low storage BFGS
nonlinear optimization in torsional angle space
MINPATH Subroutine
“minpath” is a routine for finding the triangle smoothed upper and lower bounds of each atom to a
specified root atom using a sparse variant of the Bellman-Ford shortest path algorithm
MINRIGID Program
“minrigid” performs an energy minimization of rigid body atom groups using a low storage BFGS
nonlinear optimization
MINRIGID1 Function

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“minrigid1” is a service routine that computes the energy and gradient for a low storage BFGS
nonlinear optimization of rigid bodies
MISSINF_SIGN Subroutine
“missinf_sign” takes as input the indices of three infinite points, then finds the index of the missing
fourth infinite point, and gives the signature of the permutation required to put the three infinite
points in order
MLIGHT Subroutine
“mlight” performs a complete rebuild of the atomic multipole pair neighbor list for all sites using
the method of lights
MLIST Subroutine
“mlist” performs an update or a complete rebuild of the nonbonded neighbor lists for atomic mul-
tipoles
MMID Subroutine
“mmid” implements a modified midpoint method to advance the integration of a set of first order
differential equations
MODECART Subroutine
MODERGD Subroutine
MODEROT Subroutine
MODESRCH Subroutine
MODETORS Subroutine
MODULI Subroutine
“moduli” sets the moduli of the inverse discrete Fourier transform of the B-splines
MOL2XYZ Program
“mol2xyz” takes as input a Tripos MOL2 coordinates file, converts to and then writes out Cartesian
coordinates
MOLECULE Subroutine
“molecule” counts the molecules, assigns each atom to its molecule and computes the mass of each
molecule
MOLMERGE Subroutine
“molmerge” connects fragments and removes duplicate atoms during generation of a unit cell from
an asymmetric unit
MOLSETUP Subroutine
“molsetup” generates trial parameters needed to perform polarizable multipole calculations on a
structure read from distributed multipole analysis output
MOLUIND Subroutine

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“moluind” computes the molecular induced dipole components in the presence of an external elec-
tric field
MOLXYZ Program
“molxyz” takes as input a MDL MOL coordinates file, converts to and then writes out Cartesian
coordinates
MOMENTS Subroutine
“moments” computes the total electric charge, dipole and quadrupole moments for the active atoms
as a sum over the partial charges, bond dipoles and atomic multipole moments
MOMFULL Subroutine
“momfull” computes the electric moments for the full system as a sum over the partial charges,
bond dipoles and atomic multipole moments
MOMYZE Subroutine
“momyze” finds and prints the total charge, dipole moment components, radius of gyration and
moments of inertia
MONTE Program
“monte” performs a Monte Carlo-Minimization conformational search using Cartesian single atom
or torsional move sets
MUTATE Subroutine
“mutate” constructs the hybrid hamiltonian for a specified initial state, final state and mutation
parameter “lambda”
NBLIST Subroutine
“nblist” builds and maintains nonbonded pair neighbor lists for vdw, dispersion, electrostatic and
polarization terms
NEARBY Subroutine
“nearby” finds all of the through-space neighbors of each atom for use in surface area and volume
calculations
NEEDUPDATE Subroutine
NEWATM Subroutine
“newatm” creates and defines an atom needed for the Cartesian coordinates file, but which may
not present in the original Protein Data Bank file
NEWTON Program
“newton” performs an energy minimization in Cartesian coordinate space using a truncated Newton
method
NEWTON1 Function
“newton1” is a service routine that computes the energy and gradient for truncated Newton opti-
mization in Cartesian coordinate space

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NEWTON2 Subroutine
“newton2” is a service routine that computes the sparse matrix Hessian elements for truncated
Newton optimization in Cartesian coordinate space
NEWTROT Program
“newtrot” performs an energy minimization in torsional angle space using a truncated Newton
conjugate gradient method
NEWTROT1 Function
“newtrot1” is a service routine that computes the energy and gradient for truncated Newton conju-
gate gradient optimization in torsional angle space
NEWTROT2 Subroutine
“newtrot2” is a service routine that computes the sparse matrix Hessian elements for truncated
Newton optimization in torsional angle space
NEXTARG Subroutine
“nextarg” finds the next unused command line argument and returns it in the input character string
NEXTTEXT Function
“nexttext” finds and returns the location of the first non-blank character within an input text string;
zero is returned if no such character is found
NORMAL Function
“normal” generates a random number from a normal Gaussian distribution with a mean of zero
and a variance of one
NOSE Subroutine
“nose” performs a single molecular dynamics time step via a Nose-Hoover extended system
isothermal-isobaric algorithm
NSPLINE Subroutine
“nspline” computes coefficients for an nonperiodic cubic spline with natural boundary conditions
where the first and last second derivatives are already known
NUCBASE Subroutine
“nucbase” builds the side chain for a single nucleotide base in terms of internal coordinates
NUCCHAIN Subroutine
“nucchain” builds up the internal coordinates for a nucleic acid sequence from the sugar type,
backbone and glycosidic torsional values
NUCLEIC Program
“nucleic” builds the internal and Cartesian coordinates of a polynucleotide from nucleic acid se-
quence and torsional angle values for the nucleic acid backbone and side chains
NUMBER Function

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“number” converts a text numeral into an integer value; the input string must contain only numeric
characters
NUMERAL Subroutine
“numeral” converts an input integer number into the corresponding right- or left-justified text nu-
meral
NUMGRAD Subroutine
“numgrad” computes the gradient of the objective function “fvalue” with respect to Cartesian coor-
dinates of the atoms via a one-sided or two-sided numerical differentiation
OCVM Subroutine
“ocvm” is an optimally conditioned variable metric nonlinear optimization routine without line
searches
OLDATM Subroutine
“oldatm” get the Cartesian coordinates for an atom from the Protein Data Bank file, then assigns
the atom type and atomic connectivities
OPBGUESS Function
“opbguess” sets approximate out-of-plane bend force constants based on atom type and connected
atoms
OPENEND Subroutine
“openend” opens a file on a Fortran unit such that the position is set to the bottom for appending
to the end of the file
OPREP Subroutine
“oprep” sets up the frictional and random terms needed to update positions and velocities for the
BAOAB integrator
OPTFIT Function
OPTIMIZ1 Function
“optimiz1” is a service routine that computes the energy and gradient for optimally conditioned
variable metric optimization in Cartesian coordinate space
OPTIMIZE Program
“optimize” performs energy minimization in Cartesian coordinate space using an optimally condi-
tioned variable metric method
OPTINIT Subroutine
“optinit” initializes values and keywords used by multiple structure optimization methods
OPTIROT Program
“optirot” performs an energy minimization in torsional angle space using an optimally conditioned
variable metric method
OPTIROT1 Function

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“optirot1” is a service routine that computes the energy and gradient for optimally conditioned
variable metric optimization in torsional angle space
OPTRIGID Program
“optrigid” performs an energy minimization of rigid body atom groups using an optimally condi-
tioned variable metric method
OPTRIGID1 Function
“optrigid1” is a service routine that computes the energy and gradient for optimally conditioned
variable metric optimization of rigid bodies
OPTSAVE Subroutine
“optsave” is used by the optimizers to write imtermediate coordinates and other relevant informa-
tion; also checks for user requested termination of an optimization
ORBITAL Subroutine
“orbital” finds and organizes lists of atoms in a pisystem, bonds connecting pisystem atoms and
torsions whose central atoms are both pisystem atoms
ORIENT Subroutine
“orient” computes a set of reference Cartesian coordinates in standard orientation for each rigid
body atom group
ORTHOG Subroutine
“orthog” performs an orthogonalization of an input matrix via the modified Gram-Schmidt algo-
rithm
OVERLAP Subroutine
“overlap” computes the overlap for two parallel p-orbitals given the atomic numbers and distance
of separation
PADD Function
“padd” computes the sum of the two input arguments, and sets the result to zero if the absolute
sum or relative values are less than the machine precision
PARAMYZE Subroutine
“paramyze” prints the force field parameters used in the computation of each of the potential energy
terms
PARTYZE Subroutine
“partyze” prints the energy component and number of interactions for each of the potential energy
terms
PASSB Subroutine
PASSB2 Subroutine
PASSB3 Subroutine
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PASSB5 Subroutine
PASSF Subroutine
PASSF2 Subroutine
PASSF3 Subroutine
PASSF4 Subroutine
PASSF5 Subroutine
PATH Program
“path” locates a series of structures equally spaced along a conformational pathway connecting the
input reactant and product structures; a series of constrained optimizations orthogonal to the path
is done via Lagrangian multipliers
PATH1 Function
PATHPNT Subroutine
“pathpnt” finds a structure on the synchronous transit path with the specified path value “tpath”
PATHSCAN Subroutine
“pathscan” makes a scan of a synchronous transit pathway by computing structures and energies
for specific path values
PATHVAL Subroutine
“pathval” computes the synchronous transit path value for the specified structure
PAULING Subroutine
“pauling” uses a rigid body optimization to approximately pack multiple polypeptide chains
PAULING1 Function
“pauling1” is a service routine that computes the energy and gradient for optimally conditioned
variable metric optimization of rigid bodies
PBDIRECTPOLFORCE Subroutine
PBEMPOLE Subroutine
“pbempole” calculates the permanent multipole PB energy, field, forces and torques
PBMUTUALPOLFORCE Subroutine
PDBATOM Subroutine
“pdbatom” adds an atom to the Protein Data Bank file
PDBXYZ Program
“pdbxyz” takes as input a Protein Data Bank file and then converts to and writes out a Cartesian
coordinates file and, for biopolymers, a sequence file
PIALTER Subroutine

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“pialter” modifies bond lengths and force constants according to the “planar” P-P-P bond order
values; also alters 2-fold torsional parameters based on the “nonplanar” bond orders
PICALC Subroutine
“picalc” performs a modified Pariser-Parr-Pople molecular orbital calculation for each conjugated
pisystem
PIMOVE Subroutine
“pimove” rotates the vector between atoms “list(1)” and “list(2)” so that atom 1 is at the origin and
atom 2 along the x-axis; the atoms defining the respective planes are also moved and their bond
lengths normalized
PIPLANE Subroutine
“piplane” selects the three atoms which specify the plane perpendicular to each p-orbital; the cur-
rent version will fail in certain situations, including ketenes, allenes, and isolated or adjacent triple
bonds
PISCF Subroutine
“piscf” performs an SCF molecular orbital calculation for a pisystem to determine bond orders used
in parameter scaling
PITILT Subroutine
“pitilt” calculates for each pibond the ratio of the actual p-orbital overlap integral to the ideal
overlap if the same orbitals were perfectly parallel
PLACE Subroutine
“place” finds the probe sites by putting the probe sphere tangent to each triple of neighboring atoms
PMONTE Subroutine
“pmonte” implements a Monte Carlo barostat via random trial changes in the periodic box volume
and shape
POLARGRP Subroutine
“polargrp” generates members of the polarization group of each atom and separate lists of the 1-2,
1-3 and 1-4 group connectivities
POLARIZE Program
“polarize” computes the molecular polarizability by applying an external field along each axis fol-
lowed by diagonalization of the resulting polarizability tensor
POLEDIT Program
“poledit” provides for the modification and manipulation of polarizable atomic multipole electro-
static models
POLESORT Subroutine
“polesort” sorts a set of atomic multipole parameters based on the atom types of centers involved
POLYMER Subroutine

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“polymer” tests for the presence of an infinite polymer extending across periodic boundaries
POLYP Subroutine
“polyp” is a polynomial product routine that multiplies two algebraic forms
POTENTIAL Program
“potential” calculates the electrostatic potential for a molecule at a set of grid points; optionally
compares to a target potential or optimizes electrostatic parameters
POTGRID Subroutine
“potgrid” generates electrostatic potential grid points in radially distributed shells based on the
molecular surface
POTNRG Function
POTOFF Subroutine
“potoff” clears the forcefield definition by turning off the use of each of the potential energy func-
tions
POTPOINT Subroutine
“potpoint” calculates the electrostatic potential at a grid point “i” as the total electrostatic interac-
tion energy of the system with a positive charge located at the grid point
POTSTAT Subroutine
“potstat” computes and prints statistics for the electrostatic potential over a set of grid points
POTWRT Subroutine
PRECONBLK Subroutine
“preconblk” applies a preconditioner to an atom block section of the Hessian matrix
PRECOND Subroutine
“precond” solves a simplified version of the Newton equations Ms = r, and uses the result to pre-
condition linear conjugate gradient iterations on the full Newton equations in “tnsolve”
PRESSURE Subroutine
“pressure” uses the internal virial to find the pressure in a periodic box and maintains a constant
desired pressure via a barostat method
PRESSURE2 Subroutine
“pressure2” applies a box size and velocity correction at the half time step as needed for the Monte
Carlo barostat
PRIORITY Function
“priority” decides which of a set of connected atoms should have highest priority in construction of
a local coordinate frame and returns its atom number; if all atoms are of equal priority then zero is
returned
PRMEDIT Program

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“prmedit” reformats an existing parameter file, and revises type and class numbers based on the
“atom” parameter ordering
PRMFORM Subroutine
“prmform” formats each individual parameter record to conform to a consistent text layout
PRMKEY Subroutine
“prmkey” parses a text string to extract keywords related to force field potential energy functional
forms and constants
PRMORDER Subroutine
“prmorder” places a list of atom type or class numbers into canonical order for potential energy
parameter definitions
PRMSORT Subroutine
“prmsort” places a list of atom type or class numbers into canonical order for potential energy
parameter definitions
PRMVAR Subroutine
“prmvar” determines the optimization values from the corresponding electrostatic potential energy
parameters
PRMVAR Subroutine
“prmvar” determines the optimization values from the corresponding valence potential energy pa-
rameters
PROCHAIN Subroutine
“prochain” builds up the internal coordinates for an amino acid sequence from the phi, psi, omega
and chi values
PROJCT Subroutine
PROJECT Subroutine
“project” reads locked vectors from a binary file and projects them out of the components of the set
of trial eigenvectors using the relation Y = X - U * U^T * X
PROJECTK Subroutine
“projectk” reads locked vectors from a binary file and projects them out of the components of the
set of trial eigenvectors using the relation Y = X - U * U^T * X
PROMO Subroutine
“promo” writes a banner message containing information about the Tinker version, release date
and copyright notice
PROPERTY Function
“property” takes two input snapshot frames and computes the value of the property for which the
correlation function is being accumulated
PROSIDE Subroutine

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“proside” builds the side chain for a single amino acid residue in terms of internal coordinates
PROTEIN Program
“protein” builds the internal and Cartesian coordinates of a polypeptide from amino acid sequence
and torsional angle values for the peptide backbone and side chains
PRTARC Subroutine
“prtarc” writes a Cartesian coordinates archive as either a formatted or binary file
PRTARCB Subroutine
“prtarcb” writes out a set of Cartesian coordinates for all active atoms in the CHARMM DCD binary
format
PRTARCF Subroutine
“prtarcf” writes out a set of Cartesian coordinates for all active atoms in the Tinker XYZ archive
format
PRTDYN Subroutine
“prtdyn” writes out the information needed to restart a molecular dynamics trajectory to an external
file
PRTERR Subroutine
“prterr” writes out a set of coordinates to a file prior to aborting on a serious error
PRTFIT Subroutine
“prtfit” makes a key file containing results from fitting a charge or multipole model to an electro-
static potential grid
PRTGEN Subroutine
“prtgen” writes out a set of Cartesian coordinates to an external file in a simple generic format
PRTINT Subroutine
“prtint” writes out a set of Z-matrix internal coordinates to an external file
PRTMOD Subroutine
“prtmod” writes out a set of modified Cartesian coordinates with an optional atom number offset
to an external file
PRTMOL2 Program
“prtmol2” writes out a set of coordinates in Tripos MOL2 format to an external file
PRTPDB Subroutine
“prtpdb” writes out a set of Protein Data Bank coordinates to an external file
PRTPOLE Subroutine
“prtpole” creates a coordinates file, and a key file with atomic multipoles corrected for intergroup
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PRTPRM Subroutine
“prtprm” writes out a formatted listing of the default set of potential energy parameters for a force
field
PRTSEQ Subroutine
“prtseq” writes out a biopolymer sequence to an external file with 15 residues per line and distinct
chains separated by blank lines
PRTVAL Subroutine
“prtval” writes the final valence parameter results to the standard output and appends the values
to a key file
PRTVIB Subroutine
“prtvib” writes to an external file a series of coordinate sets representing motion along a vibrational
normal mode
PRTXYZ Subroutine
“prtxyz” writes out a set of Cartesian coordinates to an external file
PSCALE Subroutine
“pscale” implements a Berendsen barostat by scaling the coordinates and box dimensions via cou-
pling to an external constant pressure bath
PSS Program
“pss” implements the potential smoothing plus search method for global optimization in Cartesian
coordinate space with local searches performed in Cartesian or torsional space
PSS1 Function
“pss1” is a service routine that computes the energy and gradient during PSS global optimization
in Cartesian coordinate space
PSS2 Subroutine
“pss2” is a service routine that computes the sparse matrix Hessian elements during PSS global
optimization in Cartesian coordinate space
PSSRGD1 Function
“pssrgd1” is a service routine that computes the energy and gradient during PSS global optimization
over rigid bodies
PSSRIGID Program
“pssrigid” implements the potential smoothing plus search method for global optimization for a set
of rigid bodies
PSSROT Program
“pssrot” implements the potential smoothing plus search method for global optimization in tor-
sional space
PSSROT1 Function

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“pssrot1” is a service routine that computes the energy and gradient during PSS global optimization
in torsional space
PSSWRITE Subroutine
PSUB Function
“psub” computes the difference of the two input arguments, and sets the result to zero if the abso-
lute difference or relative values are less than the machine precision
PTEST Subroutine
“ptest” determines the numerical virial tensor, and compares analytical to numerical values for
dE/dV and isotropic pressure
PTINCY Function
PZEXTR Subroutine
“pzextr” is a polynomial extrapolation routine used during Bulirsch-Stoer integration of ordinary
differential equations
QIROTMAT Subroutine
“qirotmat” finds a rotation matrix that describes the interatomic vector
QONVEC Subroutine
“qonvec” is a vector utility routine used during sliding block iterative matrix diagonalization
QRFACT Subroutine
“qrfact” computes the QR factorization of an m by n matrix a via Householder transformations with
optional column pivoting; the routine determines an orthogonal matrix q, a permutation matrix p,
and an upper trapezoidal matrix r with diagonal elements of nonincreasing magnitude, such that
a*p = q*r; the Householder transformation for column k, k = 1,2,. . . ,min(m,n), is of the form:
QRSOLVE Subroutine
“qrsolve” solves a*x = b and d*x = 0 in the least squares sense; used with routine “qrfact” to solve
least squares problems
QUATFIT Subroutine
“quatfit” uses a quaternion-based method to achieve the best fit superposition of two sets of coor-
dinates
RADIAL Program
“radial” finds the radial distribution function for a specified pair of atom types via analysis of a set
of coordinate frames
RANDOM Function
“random” generates a random number on [0,1] via a long period generator due to L’Ecuyer with
Bays-Durham shuffle
RANVEC Subroutine

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“ranvec” generates a unit vector in 3-dimensional space with uniformly distributed random orien-
tation
RATTLE Subroutine
“rattle” implements the first portion of the RATTLE algorithm by correcting atomic positions and
half-step velocities to maintain interatomic distance and absolute spatial constraints
RATTLE2 Subroutine
“rattle2” implements the second portion of the RATTLE algorithm by correcting the full-step veloc-
ities in order to maintain interatomic distance constraints
READBLK Subroutine
“readblk” reads in a set of snapshot frames and transfers the values to internal arrays for use in the
computation of time correlation functions
READCART Subroutine
“readcart” gets a set of Cartesian coordinates from either a formatted or binary file
READDCD Subroutine
“readdcd” reads in a set of Cartesian coordinates from an external file in CHARMM DCD binary
format
READDYN Subroutine
“readdyn” get the positions, velocities and accelerations for a molecular dynamics restart from an
external file
READGARC Subroutine
“readgarc” reads data from Gaussian archive section; each entry is terminated with a backslash
symbol
READGAU Subroutine
“readgau” reads an ab initio optimized structure, forces, Hessian and frequencies from a Gaussian
09 output file
READGDMA Subroutine
“readgdma” takes the Distributed Multipole Analysis (DMA) output in spherical harmonics from
the GDMA program and converts to Cartesian multipoles in the global coordinate frame
READINT Subroutine
“readint” gets a set of Z-matrix internal coordinates from an external file
READJUST_SPHERE Subroutine
“readjust_sphere” removes artificial spheres for UnionBall systems containing fewer than four
spheres
READMBIS Subroutine
“readmbis” takes the Minimal Basis Iterative Stockholder (MBIS) output as Cartesian multipoles
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READMOL Subroutine
“readmol” gets a set of MDL MOL coordinates from an external file
READMOL2 Subroutine
“readmol2” gets a set of Tripos MOL2 coordinates from an external file
READPDB Subroutine
“readpdb” gets a set of Protein Data Bank coordinates from an external file
READPOT Subroutine
“readpot” gets a set of grid points and target electrostatic potential values from an external file
READPRM Subroutine
“readprm” processes the potential energy parameter file in order to define the default force field
parameters
READSEQ Subroutine
“readseq” gets a biopolymer sequence containing one or more separate chains from an external file;
all lines containing sequence must begin with the starting sequence number, the actual sequence is
read from subsequent nonblank characters
READXYZ Subroutine
“readxyz” gets a set of Cartesian coordinates from an external file in either Tinker XYZ format or
simple generic XYZ format
REFINE Subroutine
“refine” performs minimization of the atomic coordinates of an initial crude embedded distance
geometry structure versus the bound, chirality, planarity and torsional error functions
REGULAR3 Subroutine
“regular3” computes the regular triangulation of a set of N weighted points in 3D using the incre-
mental flipping algorithm of Herbert Edelsbrunner
REGULAR_CONVEX Subroutine
“regular_convex” checks if a link facet (a,b,c) is locally regular, as well as if the union of the two
tetrahedra ABCP and ABCO that connect to the facet is convex
RELEASEMONITOR Subroutine
REPLICA Subroutine
“replica” decides between images and replicates for generation of periodic boundary conditions,
and sets the cell replicate list if the replicates method is to be used
RESPA Subroutine
“respa” performs a single multiple time step molecular dynamics step using the reversible reference
system propagation algorithm (r-RESPA) via a Verlet core with the potential split into fast- and
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RFINDEX Subroutine
“rfindex” finds indices for each multipole site for use in computing reaction field energetics
RGDREST Subroutine
“rgdrest” removes any translational or rotational inertia during molecular dynamics over rigid body
coordinates
RGDSTEP Subroutine
“rgdstep” performs a single molecular dynamics time step via a rigid body integration algorithm
RIBOSOME Subroutine
“ribosome” translates a polypeptide structure in Protein Data Bank format to a Cartesian coordinate
file and sequence file
RIGIDXYZ Subroutine
“rigidxyz” computes Cartesian coordinates for a rigid body group via rotation and translation of
reference coordinates
RINGS Subroutine
“rings” searches the structure for small rings and stores their constituent atoms, and optionally
reduces large rings into their component smaller rings
RMSERROR Subroutine
“rmserror” computes the maximum absolute deviation and the rms deviation from the distance
bounds, and the number and rms value of the distance restraint violations
RMSFIT Function
“rmsfit” computes the rms fit of two coordinate sets
ROTANG Function
ROTCHECK Function
“rotcheck” tests a specified candidate rotatable bond for the disallowed case where inactive atoms
are found on both sides of the candidate bond
ROTEULER Subroutine
“roteuler” computes a set of Euler angle values consistent with an input rotation matrix
ROTFRAME Subroutine
“rotframe” takes the global multipole moments and rotates them into the local coordinate frame
defined at each atomic site
ROTLIST Subroutine
“rotlist” generates the minimum list of all the atoms lying to one side of a pair of directly bonded
atoms; optionally finds the minimal list by choosing the side with fewer atoms
ROTMAT Subroutine

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“rotmat” finds the rotation matrix that rotates the local coordinate system into the global frame at
a multipole site
ROTPOLE Subroutine
“rotpole” constructs the set of atomic multipoles in the global frame by applying the correct rotation
matrix for each site
ROTRGD Subroutine
“rotrgd” finds the rotation matrix for a rigid body due to a single step of dynamics
ROTSITE Subroutine
“rotsite” rotates the local frame atomic multipoles at a specified site into the global coordinate
frame by applying a rotation matrix
SADDLE Program
“saddle” finds a transition state between two conformational minima using a combination of ideas
from the synchronous transit (Halgren-Lipscomb) and quadratic path (Bell-Crighton) methods
SADDLE1 Function
“saddle1” is a service routine that computes the energy and gradient for transition state optimiza-
tion
SADDLES Subroutine
“saddles” constructs circles, convex edges and saddle faces
SAVEYZE Subroutine
“saveyze” prints the atomic forces and/or the induced dipoles to separate external files
SBGUESS Subroutine
“sbguess” sets approximate stretch-bend force constants based on atom type and connected atoms
SCAN Program
“scan” attempts to find all the local minima on a potential energy surface via an iterative series of
local searches along normal mode directions
SCAN1 Function
“scan1” is a service routine that computes the energy and gradient during exploration of a potential
energy surface via iterative local search
SCAN2 Subroutine
“scan2” is a service routine that computes the sparse matrix Hessian elements during exploration
of a potential energy surface via iterative local search
SCANPDB Subroutine
“scanpdb” reads the first model in a Protein Data Bank file and sets chains, alternate sites and
insertion records to be used
SDAREA Subroutine

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“sdarea” optionally scales the atomic friction coefficient of each atom based on its accessible surface
area
SDSTEP Subroutine
“sdstep” performs a single stochastic dynamics time step via the velocity Verlet integration algo-
rithm
SDTERM Subroutine
“sdterm” finds the frictional and random terms needed to update positions and velocities during
stochastic dynamics
SEARCH Subroutine
“search” is a unidimensional line search based upon parabolic extrapolation and cubic interpolation
using both function and gradient values
SETACCELERATION Subroutine
SETATOMIC Subroutine
SETATOMTYPES Subroutine
SETCHARGE Subroutine
SETCHUNK Subroutine
“setchunk” marks a chunk in the PME spatial table which is overlapped by the B-splines for a site
SETCONNECTIVITY Subroutine
SETCOORDINATES Subroutine
SETELECT Subroutine
“setelect” assigns partial charge, bond dipole and atomic multipole parameters for the current
structure, as needed for computation of the electrostatic potential
SETENERGY Subroutine
SETFILE Subroutine
SETFORCEFIELD Subroutine
SETFRAME Subroutine
“setframe” assigns a local coordinate frame at each atomic multipole site using high priority con-
nected atoms along axes
SETGRADIENTS Subroutine
SETINDUCED Subroutine
SETKEYWORD Subroutine
SETMASS Subroutine
SETMDTIME Subroutine
SETMOL2 Program

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“setmol2” assigns MOL2 atom names/types/charges and bond types based upon atomic numbers
and connectivity
SETNAME Subroutine
SETPAIR Program
“setpair” is a service routine that assigns flags, sets cutoffs and allocates arrays used by different
pairwise neighbor methods
SETPOLAR Subroutine
“setpolar” assigns atomic polarizabilities, Thole damping or charge penetration parameters, and
polarization groups with user modification of these values
SETPRM Subroutine
“setprm” counts and allocates memory space for force field parameter values involving multiple
atom types or classes as found in the parameter file and keyfile
SETSTEP Subroutine
SETSTORY Subroutine
SETTIME Subroutine
“settime” initializes the wall clock and elapsed CPU times
SETUNION Subroutine
“setunion” gets the coordinates and radii of the balls, and stores these into data structures used in
UnionBall
SETUPDATED Subroutine
SETVARS Subroutine
“setvars” finds and stores nonzero partial charge, atomic multipole and charge penetration param-
eters for each atom of the current structure
SETVELOCITY Subroutine
SHAKE Subroutine
“shake” implements the SHAKE algorithm by correcting atomic positions to maintain interatomic
distance and absolute spatial constraints
SHAKE2 Subroutine
“shake2” modifies the gradient to remove components along any holonomic distance contraints
using a variant of SHAKE
SHAKEUP Subroutine
“shakeup” initializes any holonomic constraints for use with the SHAKE and RATTLE algorithms
SHROTMAT Subroutine
“shrotmat” finds the rotation matrix that converts spherical harmonic quadrupoles from the local
to the global frame given the required dipole rotation matrix

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SHROTSITE Subroutine
“shrotsite” converts spherical harmonic multipoles from the local to the global frame given required
rotation matrices
SIGMOID Function
“sigmoid” implements a normalized sigmoidal function on the interval [0,1]; the curves connect
(0,0) to (1,1) and have a cooperativity controlled by beta, they approach a straight line as beta ->
0 and get more nonlinear as beta increases
SIMPLEX Subroutine
“simplex” is a general multidimensional Nelder-Mead simplex optimization routine requiring only
repeated evaluations of the objective function
SIMPLEX1 Function
“simplex1” is a service routine used only by the Nelder-Mead simplex optimization method
SKTDYN Subroutine
“sktdyn” sends the current dynamics info via a socket
SKTINIT Subroutine
“sktinit” sets up socket communication with the graphical user interface by starting a Java virtual
machine, initiating a server, and loading an object with system information
SKTKILL Subroutine
“sktkill” closes the server and Java virtual machine
SKTOPT Subroutine
“sktopt” sends the current optimization info via a socket
SLATER Subroutine
“slater” is a general routine for computing the overlap integrals between two Slater-type orbitals
SNIFFER Program
“sniffer” performs a global energy minimization using a discrete version of Griewank’s global search
trajectory
SNIFFER1 Function
“sniffer1” is a service routine that computes the energy and gradient for the Sniffer global opti-
mization method
SOAK Subroutine
“soak” takes a currently defined solute system and places it into a solvent box, with removal of any
solvent molecules that overlap the solute
SORT Subroutine
“sort” takes an input list of integers and sorts it into ascending order using the Heapsort algorithm
SORT10 Subroutine

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“sort10” takes an input list of character strings and sorts it into alphabetical order using the Heap-
sort algorithm, duplicate values are removed from the final sorted list
SORT2 Subroutine
“sort2” takes an input list of reals and sorts it into ascending order using the Heapsort algorithm;
it also returns a key into the original ordering
SORT3 Subroutine
“sort3” takes an input list of integers and sorts it into ascending order using the Heapsort algorithm;
it also returns a key into the original ordering
SORT4 Subroutine
“sort4” takes an input list of integers and sorts it into ascending absolute value using the Heapsort
algorithm
SORT5 Subroutine
“sort5” takes an input list of integers and sorts it into ascending order based on each value modulo
“m”
SORT6 Subroutine
“sort6” takes an input list of character strings and sorts it into alphabetical order using the Heapsort
algorithm
SORT7 Subroutine
“sort7” takes an input list of character strings and sorts it into alphabetical order using the Heapsort
algorithm; it also returns a key into the original ordering
SORT8 Subroutine
“sort8” takes an input list of integers and sorts it into ascending order using the Heapsort algorithm,
duplicate values are removed from the final sorted list
SORT9 Subroutine
“sort9” takes an input list of reals and sorts it into ascending order using the Heapsort algorithm,
duplicate values are removed from the final sorted list
SPACEFILL Program
“spacefill” computes the surface area and volume of a structure; the van der Waals, accessible-
excluded, and contact-reentrant definitions are available
SPECTRUM Program
“spectrum” computes a power spectrum over a wavelength range from the velocity autocorrelation
as a function of time
SPHERE Subroutine
“sphere” finds a specified number of uniformly distributed points on a sphere of unit radius centered
at the origin
SQUARE Subroutine

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“square” is a nonlinear least squares routine derived from the IMSL BCLSF routine and the MIN-
PACK LMDER routine; the Jacobian is estimated by finite differences and bounds can be specified
for the variables to be refined
SUFFIX Subroutine
“suffix” checks a filename for the presence of an extension, and appends an extension and version
if none is found
SUPERPOSE Program
“superpose” takes pairs of structures and superimposes them in the optimal least squares sense; it
will attempt to match all atom pairs or only those specified by the user
SURFACE Subroutine
“surface” computes the weighted solvent accessible surface area each atom via the inclusion-
exclusion method of Herbert Edelsbrunner based on alpha shapes
SURFACE1 Subroutine
“surface1” computes the weighted solvent accessible surface area of each atom and the first deriva-
tives of the area with respect to Cartesian coordinates via the inclusion-exclusion method of Herbert
Edelsbrunner based on alpha shapes
SURFATOM Subroutine
“surfatom” performs an analytical computation of the surface area of a specified atom; a simplified
version of “surface”
SURFATOM1 Subroutine
“surfatom1” performs an analytical computation of the surface area and first derivatives with re-
spect to Cartesian coordinates of a specified atom
SWITCH Subroutine
“switch” sets the coeffcients used by the fifth and seventh order polynomial switching functions for
spherical cutoffs
SYMMETRY Subroutine
“symmetry” applies symmetry operators to the fractional coordinates of the asymmetric unit in
order to generate the symmetry related atoms of the full unit cell
SYSTYZE Subroutine
“systyze” is an auxiliary routine for the analyze program that prints general information about the
molecular system and the force field model
TABLE_FILL Subroutine
“table_fill” constructs an array which stores the spatial regions of the particle mesh Ewald grid with
contributions from each site
TANGENT Subroutine
“tangent” finds the projected gradient on the synchronous transit path for a point along the transit
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TCGSWAP Subroutine
“tcgswap” switches two sets of induced dipole quantities for use with the TCG induced dipole solver
TCG_ALPHA12 Subroutine
“tcg_alpha12” computes source1 = alpha*source1 and source2 = alpha*source2
TCG_ALPHA22 Subroutine
“tcg_alpha22” computes result1 = alpha*source1 and result2 = alpha*source2
TCG_ALPHAQUAD Subroutine
“tcg_alphaquad” computes the quadratic form, <a*alpha*b>, where alpha is the diagonal atomic
polarizability matrix
TCG_DOTPROD Subroutine
“tcg_dotprod” computes the dot product of two vectors of length n elements
TCG_RESOURCE Subroutine
“tcg_resource” sets the number of mutual induced dipole pairs based on the passed argument
TCG_T0 Subroutine
“tcg_t0” applies T matrix to ind/p, and returns v3d/p T = 1/alpha + Tu
TCG_UFIELD Subroutine
“tcg_ufield” applies -Tu to ind/p and returns v3d/p
TCG_UPDATE Subroutine
“tcg_update” computes pvec = alpha*rvec + beta*pvec; if the preconditioner is not used, then
alpha = identity
TEMPER Subroutine
“temper” computes the instantaneous temperature and applies a thermostat via Berendsen or Bussi-
Parrinello velocity scaling, Andersen stochastic collisions or Nose-Hoover chains; also uses Berend-
sen scaling for any iEL induced dipole variables
TEMPER2 Subroutine
“temper2” applies a velocity correction at the half time step as needed for the Nose-Hoover ther-
mostat
TESTGRAD Program
“testgrad” computes and compares the analytical and numerical gradient vectors of the potential
energy function with respect to Cartesian coordinates
TESTHESS Program
“testhess” computes and compares the analytical and numerical Hessian matrices of the potential
energy function with respect to Cartesian coordinates
TESTPAIR Program

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“testpair” performs a set of timing tests to compare the evaluation of potential energy and en-
ergy/gradient using different methods for finding pairwise neighbors
TESTPOL Program
“testpol” compares the induced dipoles from direct polarization, mutual SCF iterations, perturba-
tion theory extrapolation (OPT), and truncated conjugate gradient (TCG) solvers
TESTROT Program
“testrot” computes and compares the analytical and numerical gradient vectors of the potential
energy function with respect to rotatable torsional angles
TESTVIR Program
“testvir” computes the analytical internal virial and compares it to a numerical virial derived from
the finite difference derivative of the energy with respect to lattice vectors
TETTORS Subroutine
“tettors” finds the total number of tetratorsions as tuples of adjacent torsional angles, and the
numbers of the seven atoms defining each tetratorsion
TIMER Program
“timer” measures the CPU time required for file reading and parameter assignment, potential en-
ergy computation, energy and gradient computation, and Hessian matrix evaluation
TIMEROT Program
“timerot” measures the CPU time required for file reading and parameter assignment, potential
energy computation, energy and gradient over torsions, and torsional angle Hessian matrix evalu-
ation
TNCG Subroutine
“tncg” implements a truncated Newton optimization algorithm in which a preconditioned linear
conjugate gradient method is used to approximately solve Newton’s equations; special features
include use of an explicit sparse Hessian or finite-difference gradient-Hessian products within the
PCG iteration; the exact Newton search directions can be used optionally; by default the algo-
rithm checks for negative curvature to prevent convergence to a stationary point having negative
eigenvalues; if a saddle point is desired this test can be removed by disabling “negtest”
TNSOLVE Subroutine
“tnsolve” uses a linear conjugate gradient method to find an approximate solution to the set of
linear equations represented in matrix form by Hp = -g (Newton’s equations)
TORFIT1 Function
“torfit1” is a service routine that computes the energy and gradient for a low storage BFGS opti-
mization in Cartesian coordinate space
TORGUESS Subroutine
“torguess” set approximate torsion amplitude parameters based on atom type and connected atoms
TORPHASE Subroutine

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“torphase” sets the n-fold amplitude and phase values for each torsion via sorting of the input
parameters
TORQUE Subroutine
“torque” takes the torque values on a single site defined by a local coordinate frame and converts
to Cartesian forces on the original site and sites specifying the local frame, also gives the x,y,z-force
components needed for virial computation
TORSER Function
“torser” computes the torsional error function and its first derivatives with respect to the atomic
Cartesian coordinates based on the deviation of specified torsional angles from desired values, the
contained bond angles are also restrained to avoid a numerical instability
TORSFIT Program
“torsfit” refines torsional force field parameters based on a quantum mechanical potential surface
and analytical gradient
TORSIONS Subroutine
“torsions” finds the total number of torsional angles and the numbers of the four atoms defining
each torsional angle
TORUS Subroutine
“torus” sets a list of all of the temporary torus positions by testing for a torus between each atom
and its neighbors
TOTERR Function
“toterr” is the error function and derivatives for a distance geometry embedding; it includes com-
ponents from the distance bounds, hard sphere contacts, local geometry, chirality and torsional
restraint errors
TRANSFORM Subroutine
“transform” diagonalizes the current basis vectors to produce trial roots for sliding block iterative
matrix diagonalization
TRANSIT Function
“transit” evaluates the synchronous transit function and gradient; linear and quadratic transit paths
are available
TRBASIS Subroutine
“trbasis” forms translation and rotation basis vectors used during vibrational analysis via block
iterative diagonalization
TRIANGLE Subroutine
“triangle” smooths the upper and lower distance bounds via the triangle inequality using a full-
matrix variant of the Floyd-Warshall shortest path algorithm; this routine is usually much slower
than the sparse matrix shortest path methods in “geodesic” and “trifix”, and should be used only
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TRIANGLE_ATTACH Subroutine
“triangle_attach” tests whether a point D is inside the circumsphere defined by three other points
A, B and C
TRIANGLE_RADIUS Subroutine
“triangle_radius” computes the radius of the smallest circumsphere to a triangle
TRIFIX Subroutine
“trifix” rebuilds both the upper and lower distance bound matrices following tightening of one
or both of the bounds between a specified pair of atoms, “p” and “q”, using a modification of
Murchland’s shortest path update algorithm
TRIGGER Subroutine
“trigger” constructs a set of initial trial vectors for use during sliding block iterative matrix diago-
nalization
TRIMHEAD Subroutine
“trimhead” removes blank spaces before the first non-blank character in a text string by shifting the
string to the left
TRIMTEXT Function
“trimtext” finds and returns the location of the last non-blank character before the first null charac-
ter in an input text string; the function returns zero if no such character is found
TRIPLE Function
“triple” finds the triple product of three vectors; used as a service routine by the Connolly surface
area and volume computation
TRITORS Subroutine
“tritors” finds the total number of tritorsions as triples of adjacent torsional angles, and the numbers
of the six atoms defining each tritorsion
TRUST Subroutine
“trust” updates the model trust region for a nonlinear least squares calculation based on ideas found
in NL2SOL and Dennis and Schnabel’s book
UBUILD Subroutine
“ubuild” performs a complete rebuild of the polarization preconditioner neighbor list for all sites
UDIRECT1 Subroutine
“udirect1” computes the reciprocal space contribution of the permanent atomic multipole moments
to the field
UDIRECT2A Subroutine
“udirect2a” computes the real space contribution of the permanent atomic multipole moments to
the field via a double loop
UDIRECT2B Subroutine

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“udirect2b” computes the real space contribution of the permanent atomic multipole moments to
the field via a neighbor list
UFIELD0A Subroutine
“ufield0a” computes the mutual electrostatic field due to induced dipole moments via a double loop
UFIELD0B Subroutine
“ufield0b” computes the mutual electrostatic field due to induced dipole moments via a pair list
UFIELD0C Subroutine
“ufield0c” computes the mutual electrostatic field due to induced dipole moments via Ewald sum-
mation
UFIELD0D Subroutine
“ufield0d” computes the mutual electrostatic field due to induced dipole moments for use with with
generalized Kirkwood implicit solvation
UFIELD0E Subroutine
“ufield0e” computes the mutual electrostatic field due to induced dipole moments via a Poisson-
Boltzmann solver
UFIELDI Subroutine
“ufieldi” computes the electrostatic field due to intergroup induced dipole moments
ULIGHT Subroutine
“ulight” performs a complete rebuild of the polarization preconditioner pair neighbor list for all
sites using the method of lights
ULIST Subroutine
“ulist” performs an update or a complete rebuild of the neighbor lists for the polarization precon-
ditioner
ULSPRED Subroutine
“ulspred” uses standard extrapolation or a least squares fit to set coefficients of an induced dipole
predictor polynomial
UMUTUAL1 Subroutine
“umutual1” computes the reciprocal space contribution of the induced atomic dipole moments to
the field
UMUTUAL2A Subroutine
“umutual2a” computes the real space contribution of the induced atomic dipole moments to the
field via a double loop
UMUTUAL2B Subroutine
“umutual2b” computes the real space contribution of the induced atomic dipole moments to the
field via a neighbor list

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UNIONBALL Subroutine
“unionball” computes the surface area and volume of a union of balls via the analytical inclusion-
exclusion method of Herbert Edelsbrunner based on alpha shapes, also finds derivatives of surface
area and volume with respect to Cartesian coordinates
UNITCELL Subroutine
“unitcell” gets the periodic boundary box size and related values from an external keyword file
UPCASE Subroutine
“upcase” converts a text string to all upper case letters
URYGUESS Function
“uryguess” sets approximate Urey-Bradley force constants based on atom type and connected atoms
USCALE0A Subroutine
“uscale0a” builds and applies a preconditioner for the conjugate gradient induced dipole solver
using a double loop
USCALE0B Subroutine
“uscale0b” builds and applies a preconditioner for the conjugate gradient induced dipole solver
using a neighbor pair list
VALENCE Program
“valence” refines force field parameters for valence terms based on a quantum mechanical opti-
mized structure and frequencies
VALFIT1 Function
“valfit1” is a service routine that computes the RMS error and gradient for valence parameters fit
to QM results
VALGUESS Subroutine
“valguess” sets approximate valence parameter values based on quantum mechanical structure and
frequency data
VALMIN1 Function
“valmin1” is a service routine that computes the molecular energy and gradient during valence
parameter optimization
VALRMS Function
“valrms” evaluates a valence parameter goodness-of-fit error function based on comparison of
forces, frequencies, bond lengths and angles to QM results
VALSORT2 Subroutine
“valsort2” sorts numbers A and B, where input values are kept unaffected, and new output values
are generated
VALSORT3 Subroutine

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“valsort3” sorts numbers A, B and C, where input values are kept unaffected, and new output values
are generated
VALSORT4 Subroutine
“valsort4” sorts numbers A, B, C and D, where input values are kept unaffected, and new output
values are generated
VALSORT5 Subroutine
“valsort5” sorts numbers A, B, C, D and E, where input values are kept unaffected, and new output
values are generated
VAM Subroutine
“vam” takes the analytical molecular surface defined as a collection of spherical and toroidal poly-
gons and uses it to compute the volume and surface area
VARPRM Subroutine
“varprm” copies the current optimization values into the corresponding electrostatic potential en-
ergy parameters
VARPRM Subroutine
“varprm” copies the current optimization values into the corresponding valence potential energy
parameters
VBUILD Subroutine
“vbuild” performs a complete rebuild of the van der Waals pair neighbor list for all sites
VCROSS Subroutine
“vcross” finds the cross product of two vectors
VDWERR Function
“vdwerr” is the hard sphere van der Waals bound error function and derivatives that penalizes close
nonbonded contacts, pairwise neighbors are generated via the method of lights
VDWGUESS Subroutine
“vdwguess” sets initial VDW parameters based on atom type and connected atoms
VECANG Function
“vecang” finds the angle between two vectors handed with respect to a coordinate axis; returns an
angle in the range [0,2*pi]
VERLET Subroutine
“verlet” performs a single molecular dynamics time step via the velocity Verlet multistep recursion
formula
VERSION Subroutine
“version” checks the name of a file about to be opened; if if “old” status is passed, the name of
the highest current version is returned; if “new” status is passed the filename of the next available
unused version is generated

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VERTEX_ATTACH Subroutine
“vertex_attach” tests for a vertex is attached to another vertex, the computation is done in both
directions
VIBBIG Program
“vibbig” performs large-scale vibrational mode analysis using only vector storage and gradient eval-
uations; preconditioning is via an approximate inverse from a block diagonal Hessian, and a sliding
block method is used to converge any number of eigenvectors starting from either lowest or highest
frequency
VIBRATE Program
“vibrate” performs a vibrational normal mode analysis; the Hessian matrix of second derivatives is
determined and then diagonalized both directly and after mass weighting; output consists of the
eigenvalues of the force constant matrix as well as the vibrational frequencies and displacements
VIBROT Program
“vibrot” computes the eigenvalues and eigenvectors of the torsional Hessian matrix
VIRIYZE Subroutine
“propyze” finds and prints the internal virial, the dE/dV value and an estimate of the pressure
VLIGHT Subroutine
“vlight” performs a complete rebuild of the van der Waals pair neighbor list for all sites using the
method of lights
VLIST Subroutine
“vlist” performs an update or a complete rebuild of the nonbonded neighbor lists for vdw sites
VNORM Subroutine
“vnorm” normalizes a vector to unit length; used as a service routine by the Connolly surface area
and volume computation
VOLUME Subroutine
“volume” computes the weighted solvent excluded volume via the inclusion-exclusion method of
Herbert Edelsbrunner based on alpha shapes; also finds the accessible surface area
VOLUME1 Subroutine
“volume1” computes the weighted solvent excluded volume and the first derivatives of the volume
with respect to Cartesian coordinates via the inclusion-exclusion method of Herbert Edelsbrunner
based on alpha shapes; also finds the accessible surface area and first derivatives
VOLUME2 Subroutine
“volume2” calculates second derivatives of the total excluded volume with respect to the Cartesian
coordinates of the atoms
WATSON Subroutine

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“watson” uses a rigid body optimization to approximately align the paired strands of a nucleic acid
double helix
WATSON1 Function
“watson1” is a service routine that computes the energy and gradient for optimally conditioned
variable metric optimization of rigid bodies
WIGGLE Subroutine
“wiggle” applies a small random perturbation of coordinates to avoid numerical instability in geo-
metric calculations for linear, planar and other symmetric structures
XTALERR Subroutine
“xtalerr” computes an error function value derived from lattice energies, dimer intermolecular
energies and the gradient with respect to structural parameters
XTALFIT Program
“xtalfit” determines optimized van der Waals and electrostatic parameters by fitting to crystal struc-
tures, lattice energies, and dimer structures and interaction energies
XTALMIN Program
“xtalmin” performs a full crystal energy minimization by optimizing over fractional atomic coordi-
nates and the six lattice lengths and angles
XTALMIN1 Function
“xtalmin1” is a service routine that computes the energy and gradient with respect to fractional
coordinates and lattice dimensions for a crystal energy minimization
XTALMOVE Subroutine
“xtalmove” converts fractional to Cartesian coordinates for rigid molecules during optimization of
force field parameters
XTALPRM Subroutine
“xtalprm” stores or retrieves a molecular structure; used to make a previously stored structure the
active structure, or to store a structure for later use
XTALWRT Subroutine
“xtalwrt” prints intermediate results during fitting of force field parameters to structures and ener-
gies
XYZATM Subroutine
“xyzatm” computes the Cartesian coordinates of a single atom from its defining internal coordinate
values
XYZEDIT Program
“xyzedit” provides for modification and manipulation of the contents of Cartesian coordinates files
XYZINT Program

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“xyzint” takes as input a Cartesian coordinates file, then converts to and writes out an internal
coordinates file
XYZMOL2 Program
“xyzmol2” takes as input a Cartesian coordinates file, converts to and then writes out a Tripos MOL2
file
XYZPDB Program
“xyzpdb” takes as input a Cartesian coordinates file, then converts to and writes out a Protein Data
Bank file
XYZREST Subroutine
“xyzrest” removes any translational or rotational inertia during molecular dynamics for the overall
system or atom groups
XYZRIGID Subroutine
“xyzrigid” computes the center of mass and Euler angle rigid body coordinates for each atom group
in the system
ZATOM Subroutine
“zatom” adds an atom to the end of the current Z-matrix and then increments the atom counter;
atom type, defining atoms and internal coordinates are passed as arguments
ZHELP Subroutine
“zhelp” prints the general information and instructions for the Z-matrix editing program
ZVALUE Subroutine
“zvalue” gets user supplied values for selected coordinates as needed by the internal coordinate
editing program

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 CHAPTER

TEN

MODULES & GLOBAL VARIABLES

The Fortran modules found in the Tinker package are listed below along with a brief description
of the variables associated with each module. Each individual module contains a set of globally
allocated variables available to any program unit upon inclusion of that module. A source listing
containing each of the Tinker functions and subroutines and its included modules can be produced
by running the “listing.make” script found in the distribution.
ACTION Module total number of each energy term type

neb number of bond stretch energy terms computed

nea number of angle bend energy terms computed
neba number of stretch-bend energy terms computed
neub number of Urey-Bradley energy terms computed
neaa number of angle-angle energy terms computed
neopb number of out-of-plane bend energy terms computed
neopd number of out-of-plane distance energy terms computed
neid number of improper dihedral energy terms computed
neit number of improper torsion energy terms computed
net number of torsional energy terms computed
nept number of pi-system torsion energy terms computed
nebt number of stretch-torsion energy terms computed
neat number of angle-torsion energy terms computed
nett number of torsion-torsion energy terms computed
nev number of van der Waals energy terms computed
ner number of Pauli repulsion energy terms computed
nedsp number of dispersion energy terms computed
nec number of charge-charge energy terms computed
necd number of charge-dipole energy terms computed
ned number of dipole-dipole energy terms computed
nem number of multipole energy terms computed
nep number of polarization energy terms computed
nect number of charge transfer energy terms computed
new number of Ewald summation energy terms computed
nerxf number of reaction field energy terms computed
nes number of solvation energy terms computed
nelf number of metal ligand field energy terms computed
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(continued from previous page)

neg number of geometric restraint energy terms computed
nex number of extra energy terms computed

ALFMOL Module AlphaMol area and volume information

alfthread number of OpenMP threads to use for AlphaMol2

delcxeps eps value for AlphaMol Delaunay triangulation
alfhydro logical flag to include hydrogen atoms in AlphaMol
alfsosgmp logical flag governing use of SoS GMP in AlphaMol
alfmethod set AlphaMol1 or AlphaMol2 (SINGLE or MULTI threaded)
alfsort set sort method (NONE, Sort3D, BRIO, Split, KDTree)

ALIGN Module information for structure superposition

nfit number of atoms to use in superimposing two structures

ifit atom numbers of pairs of atoms to be superimposed
wfit weights assigned to atom pairs during superposition

ANALYZ Module energy components partitioned to atoms

aesum total potential energy partitioned over atoms

aeb bond stretch energy partitioned over atoms
aea angle bend energy partitioned over atoms
aeba stretch-bend energy partitioned over atoms
aeub Urey-Bradley energy partitioned over atoms
aeaa angle-angle energy partitioned over atoms
aeopb out-of-plane bend energy partitioned over atoms
aeopd out-of-plane distance energy partitioned over atoms
aeid improper dihedral energy partitioned over atoms
aeit improper torsion energy partitioned over atoms
aet torsional energy partitioned over atoms
aept pi-system torsion energy partitioned over atoms
aebt stretch-torsion energy partitioned over atoms
aeat angle-torsion energy partitioned over atoms
aett torsion-torsion energy partitioned over atoms
aev van der Waals energy partitioned over atoms
aer Pauli repulsion energy partitioned over atoms
aedsp damped dispersion energy partitioned over atoms
aec charge-charge energy partitioned over atoms
aecd charge-dipole energy partitioned over atoms
aed dipole-dipole energy partitioned over atoms
aem multipole energy partitioned over atoms
aep polarization energy partitioned over atoms
aect charge transfer energy partitioned over atoms
aerxf reaction field energy partitioned over atoms
aes solvation energy partitioned over atoms
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(continued from previous page)

aelf metal ligand field energy partitioned over atoms
aeg geometric restraint energy partitioned over atoms
aex extra energy term partitioned over atoms

ANGANG Module angle-angles in current structure

nangang total number of angle-angle interactions

iaa angle numbers used in each angle-angle term
kaa force constant for angle-angle cross terms

ANGBND Module bond angle bends in current structure

nangle total number of angle bends in the system

iang numbers of the atoms in each angle bend
ak harmonic angle force constant (kcal/mole/rad**2)
anat ideal bond angle or phase shift angle (degrees)
afld periodicity for Fourier angle bending term

ANGPOT Module angle bend functional form details

angunit convert angle bending energy to kcal/mole

stbnunit convert stretch-bend energy to kcal/mole
aaunit convert angle-angle energy to kcal/mole
opbunit convert out-of-plane bend energy to kcal/mole
opdunit convert out-of-plane distance energy to kcal/mole
cang cubic coefficient in angle bending potential
qang quartic coefficient in angle bending potential
pang quintic coefficient in angle bending potential
sang sextic coefficient in angle bending potential
copb cubic coefficient in out-of-plane bend potential
qopb quartic coefficient in out-of-plane bend potential
popb quintic coefficient in out-of-plane bend potential
sopb sextic coefficient in out-of-plane bend potential
copd cubic coefficient in out-of-plane distance potential
qopd quartic coefficient in out-of-plane distance potential
popd quintic coefficient in out-of-plane distance potential
sopd sextic coefficient in out-of-plane distance potential
opbtyp type of out-of-plane bend potential energy function
angtyp type of angle bending function for each bond angle

ANGTOR Module angle-torsions in current structure

nangtor total number of angle-torsion interactions

iat torsion and angle numbers used in angle-torsion
kant 1-, 2- and 3-fold angle-torsion force constants

ARGUE Module command line arguments at run time

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maxarg maximum number of command line arguments

narg number of command line arguments to the program
listarg flag to mark available command line arguments
arg strings containing the command line arguments

ASCII Module selected ASCII character code values

null decimal value of ASCII code for null (0)

tab decimal value of ASCII code for tab (9)
linefeed decimal value of ASCII code for linefeed (10)
formfeed decimal value of ASCII code for formfeed (12)
carriage decimal value of ASCII code for carriage return (13)
escape decimal value of ASCII code for escape (27)
space decimal value of ASCII code for blank space (32)
exclamation decimal value of ASCII code for exclamation (33)
quote decimal value of ASCII code for double quote (34)
pound decimal value of ASCII code for pound sign (35)
dollar decimal value of ASCII code for dollar sign (36)
percent decimal value of ASCII code for percent sign (37)
ampersand decimal value of ASCII code for ampersand (38)
apostrophe decimal value of ASCII code for single quote (39)
asterisk decimal value of ASCII code for asterisk (42)
plus decimal value of ASCII code for plus sign (43)
comma decimal value of ASCII code for comma (44)
minus decimal value of ASCII code for minus sign (45)
period decimal value of ASCII code for period (46)
frontslash decimal value of ASCII codd for frontslash (47)
colon decimal value of ASCII code for colon (58)
semicolon decimal value of ASCII code for semicolon (59)
equal decimal value of ASCII code for equal sign (61)
question decimal value of ASCII code for question mark (63)
atsign decimal value of ASCII code for at sign (64)
backslash decimal value of ASCII code for backslash (92)
caret decimal value of ASCII code for caret (94)
underbar decimal value of ASCII code for underbar (95)
vertical decimal value of ASCII code for vertical bar (124)
tilde decimal value of ASCII code for tilde (126)
nbsp decimal value of ASCII code for nobreak space (255)

ATMLST Module bond and angle local geometry indices

bndlist numbers of the bonds involving each atom

anglist numbers of the angles centered on each atom
balist numbers of the bonds comprising each angle

ATOMID Module atomic properties for current atoms

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tag integer atom labels from input coordinates file

class atom class number for each atom in the system
atomic atomic number for each atom in the system
valnum valence number for each atom in the system
mass atomic weight for each atom in the system
name atom name for each atom in the system
tier tier name (residue, motif, etc.) for each atom
story descriptive type for each atom in the system

ATOMS Module number, position and type of atoms

n total number of atoms in the current system

type atom type number for each atom in the system
x current x-coordinate for each atom in the system
y current y-coordinate for each atom in the system
z current z-coordinate for each atom in the system

BATH Module thermostat and barostat control values

maxnose maximum length of Nose-Hoover thermostat chain

voltrial mean number of steps between Monte Carlo moves
kelvin target value for the system temperature (K)
atmsph target value for the system pressure (atm)
tautemp time constant for Berendsen thermostat (psec)
taupres time constant for Berendsen barostat (psec)
compress isothermal compressibility of medium (atm-1)
collide collision frequency for Andersen thermostat
eta velocity value for Bussi-Parrinello barostat
volmove maximum volume move for Monte Carlo barostat (Ang**3)
vbar velocity of log volume for Nose-Hoover barostat
qbar mass of the volume for Nose-Hoover barostat
gbar force for the volume for Nose-Hoover barostat
vnh velocity of each chained Nose-Hoover thermostat
qnh mass for each chained Nose-Hoover thermostat
gnh force for each chained Nose-Hoover thermostat
isothermal logical flag governing use of temperature control
isobaric logical flag governing use of pressure control
anisotrop logical flag governing use of anisotropic pressure
thermostat choice of temperature control method to be used
barostat choice of pressure control method to be used
volscale choice of scaling method for Monte Carlo barostat

BITOR Module bitorsions in the current structure

nbitor total number of bitorsions in the system

ibitor numbers of the atoms in each bitorsion

BNDPOT Module bond stretch functional form details

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cbnd cubic coefficient in bond stretch potential

qbnd quartic coefficient in bond stretch potential
bndunit convert bond stretch energy to kcal/mole
bndtyp type of bond stretch potential energy function

BNDSTR Module bond stretches in the current structure

nbond total number of bond stretches in the system

ibnd numbers of the atoms in each bond stretch
bk bond stretch force constants (kcal/mole/Ang**2)
bl ideal bond length values in Angstroms

BOUND Module periodic boundary condition controls

polycut cutoff distance for infinite polymer nonbonds

polycut2 square of infinite polymer nonbond cutoff
use_bounds flag to use periodic boundary conditions
use_replica flag to use replicates for periodic system
use_polymer flag to mark presence of infinite polymer
use_wrap flag to wrap coordinates in output files

BOXES Module periodic boundary condition parameters

xbox length of a-axis of periodic box in Angstroms

ybox length of b-axis of periodic box in Angstroms
zbox length of c-axis of periodic box in Angstroms
alpha angle between b- and c-axes of box in degrees
beta angle between a- and c-axes of box in degrees
gamma angle between a- and b-axes of box in degrees
xbox2 half of the a-axis length of periodic box
ybox2 half of the b-axis length of periodic box
zbox2 half of the c-axis length of periodic box
box34 three-fourths axis length of truncated octahedron
volbox volume in Ang**3 of the periodic box
alpha_sin sine of the alpha periodic box angle
alpha_cos cosine of the alpha periodic box angle
beta_sin sine of the beta periodic box angle
beta_cos cosine of the beta periodic box angle
gamma_sin sine of the gamma periodic box angle
gamma_cos cosine of the gamma periodic box angle
beta_term term used in generating triclinic box
gamma_term term used in generating triclinic box
lvec real space lattice vectors as matrix rows
recip reciprocal lattice vectors as matrix columns
orthogonal flag to mark periodic box as orthogonal
monoclinic flag to mark periodic box as monoclinic
triclinic flag to mark periodic box as triclinic
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octahedron flag to mark box as truncated octahedron
dodecadron flag to mark box as rhombic dodecahedron
nonprism flag to mark octahedron or dodecahedron
nosymm flag to mark use or lack of lattice symmetry
spacegrp space group symbol for the unit cell type

CELL Module replicated cell periodic boundaries

ncell total number of cell replicates for periodic boundaries

icell offset along axes for each replicate periodic cell
xcell length of the a-axis of the complete replicated cell
ycell length of the b-axis of the complete replicated cell
zcell length of the c-axis of the complete replicated cell
xcell2 half the length of the a-axis of the replicated cell
ycell2 half the length of the b-axis of the replicated cell
zcell2 half the length of the c-axis of the replicated cell

CFLUX Module charge flux terms in current system

bflx bond stretching charge flux constant (electrons/Ang)

aflx angle bending charge flux constant (electrons/radian)
abflx asymmetric stretch charge flux constant (electrons/Ang)

CHARGE Module partial charges in current structure

nion total number of partial charges in system

iion number of the atom site for each partial charge
jion neighbor generation site for each partial charge
kion cutoff switching site for each partial charge
pchg current atomic partial charge values (e-)
pchg0 original partial charge values for charge flux

CHGPEN Module charge penetration in current structure

ncp total number of charge penetration sites in system

pcore number of core electrons at each multipole site
pval number of valence electrons at each multipole site
pval0 original number of valence electrons for charge flux
palpha charge penetration damping at each multipole site

CHGPOT Module charge-charge functional form details

electric energy factor in kcal/mole for current force field

dielec dielectric constant for electrostatic interactions
ebuffer electrostatic buffering constant added to distance
c1scale factor by which 1-1 charge interactions are scaled
c2scale factor by which 1-2 charge interactions are scaled
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c3scale factor by which 1-3 charge interactions are scaled
c4scale factor by which 1-4 charge interactions are scaled
c5scale factor by which 1-5 charge interactions are scaled
neutnbr logical flag governing use of neutral group neighbors
neutcut logical flag governing use of neutral group cutoffs

CHGTRN Module charge transfer for current structure

nct total number of dispersion sites in the system

chgct charge for charge transfer at each multipole site
dmpct charge transfer damping factor at each multipole site

CHRONO Module clock time values for current program

twall current processor wall clock time in seconds

tcpu elapsed cpu time from start of program in seconds

CHUNKS Module PME grid spatial decomposition values

nchunk total number of spatial regions for PME grid

nchk1 number of spatial regions along the a-axis
nchk2 number of spatial regions along the b-axis
nchk3 number of spatial regions along the c-axis
ngrd1 number of grid points per region along a-axis
ngrd2 number of grid points per region along b-axis
ngrd3 number of grid points per region along c-axis
nlpts PME grid points to the left of center point
nrpts PME grid points to the right of center point
grdoff offset for index into B-spline coefficients
pmetable PME grid spatial regions involved for each site

COUPLE Module atom neighbor connectivity lists

n12 number of atoms directly bonded to each atom

n13 number of atoms in a 1-3 relation to each atom
n14 number of atoms in a 1-4 relation to each atom
n15 number of atoms in a 1-5 relation to each atom
i12 atom numbers of atoms 1-2 connected to each atom
i13 atom numbers of atoms 1-3 connected to each atom
i14 atom numbers of atoms 1-4 connected to each atom
i15 atom numbers of atoms 1-5 connected to each atom

CTRPOT Module charge transfer functional form details

ctrntyp type of charge transfer term (SEPARATE or COMBINED)

DERIV Module Cartesian coord derivative components

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desum total energy Cartesian coordinate derivatives

deb bond stretch Cartesian coordinate derivatives
dea angle bend Cartesian coordinate derivatives
deba stretch-bend Cartesian coordinate derivatives
deub Urey-Bradley Cartesian coordinate derivatives
deaa angle-angle Cartesian coordinate derivatives
deopb out-of-plane bend Cartesian coordinate derivatives
deopd out-of-plane distance Cartesian coordinate derivatives
deid improper dihedral Cartesian coordinate derivatives
deit improper torsion Cartesian coordinate derivatives
det torsional Cartesian coordinate derivatives
dept pi-system torsion Cartesian coordinate derivatives
debt stretch-torsion Cartesian coordinate derivatives
deat angle-torsion Cartesian coordinate derivatives
dett torsion-torsion Cartesian coordinate derivatives
dev van der Waals Cartesian coordinate derivatives
der Pauli repulsion Cartesian coordinate derivatives
dedsp damped dispersion Cartesian coordinate derivatives
dec charge-charge Cartesian coordinate derivatives
decd charge-dipole Cartesian coordinate derivatives
ded dipole-dipole Cartesian coordinate derivatives
dem multipole Cartesian coordinate derivatives
dep polarization Cartesian coordinate derivatives
dect charge transfer Cartesian coordinate derivatives
derxf reaction field Cartesian coordinate derivatives
des solvation Cartesian coordinate derivatives
delf metal ligand field Cartesian coordinate derivatives
deg geometric restraint Cartesian coordinate derivatives
dex extra energy term Cartesian coordinate derivatives

DIPOLE Module bond dipoles in current structure

ndipole total number of dipoles in the system

idpl numbers of atoms that define each dipole
bdpl magnitude of each of the dipoles (Debye)
sdpl position of each dipole between defining atoms

DISGEO Module distance geometry bounds & parameters

vdwmax maximum value of hard sphere sum for an atom pair

compact index of local distance compaction on embedding
pathmax maximum value of upper bound after smoothing
dbnd distance geometry upper and lower bounds matrix
georad hard sphere radii for distance geometry atoms
use_invert flag to use enantiomer closest to input structure
use_anneal flag to use simulated annealing refinement

DISP Module damped dispersion for current structure

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ndisp total number of dispersion sites in the system

idisp number of the atom for each dispersion site
csixpr pairwise sum of C6 dispersion coefficients
csix C6 dispersion coefficient value at each site
adisp alpha dispersion damping value at each site

DMA Module QM spherical harmonic multipole moments

mp atomic monopole charge values from DMA

dpx atomic dipole moment x-component from DMA
dpy atomic dipole moment y-component from DMA
dpz atomic dipole moment z-component from DMA
q20 atomic Q20 quadrupole component from DMA (zz)
q21c atomic Q21c quadrupole component from DMA (xz)
q21s atomic Q21s quadrupole component from DMA (yz)
q22c atomic Q22c quadrupole component from DMA (xx-yy)
q22s atomic Q22s quadrupole component from DMA (xy)

DOMEGA Module derivative components over torsions

tesum total energy derivatives over torsions

teb bond stretch derivatives over torsions
tea angle bend derivatives over torsions
teba stretch-bend derivatives over torsions
teub Urey-Bradley derivatives over torsions
teaa angle-angle derivatives over torsions
teopb out-of-plane bend derivatives over torsions
teopd out-of-plane distance derivatives over torsions
teid improper dihedral derivatives over torsions
teit improper torsion derivatives over torsions
tet torsional derivatives over torsions
tept pi-system torsion derivatives over torsions
tebt stretch-torsion derivatives over torsions
teat angle-torsion derivatives over torsions
tett torsion-torsion derivatives over torsions
tev van der Waals derivatives over torsions
ter Pauli repulsion derivatives over torsions
tedsp dampled dispersion derivatives over torsions
tec charge-charge derivatives over torsions
tecd charge-dipole derivatives over torsions
ted dipole-dipole derivatives over torsions
tem atomic multipole derivatives over torsions
tep polarization derivatives over torsions
tect charge transfer derivatives over torsions
terxf reaction field derivatives over torsions
tes solvation derivatives over torsions
telf metal ligand field derivatives over torsions
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teg geometric restraint derivatives over torsions
tex extra energy term derivatives over torsions

DSPPOT Module dispersion interaction scale factors

dsp2scale scale factor for 1-2 dispersion energy interactions

dsp3scale scale factor for 1-3 dispersion energy interactions
dsp4scale scale factor for 1-4 dispersion energy interactions
dsp5scale scale factor for 1-5 dispersion energy interactions
use_dcorr flag to use long range dispersion correction

ENERGI Module individual potential energy components

esum total potential energy of the system

eb bond stretch potential energy of the system
ea angle bend potential energy of the system
eba stretch-bend potential energy of the system
eub Urey-Bradley potential energy of the system
eaa angle-angle potential energy of the system
eopb out-of-plane bend potential energy of the system
eopd out-of-plane distance potential energy of the system
eid improper dihedral potential energy of the system
eit improper torsion potential energy of the system
et torsional potential energy of the system
ept pi-system torsion potential energy of the system
ebt stretch-torsion potential energy of the system
eat angle-torsion potential energy of the system
ett torsion-torsion potential energy of the system
ev van der Waals potential energy of the system
er Pauli repulsion potential energy of the system
edsp dampled dispersion potential energy of the system
ec charge-charge potential energy of the system
ecd charge-dipole potential energy of the system
ed dipole-dipole potential energy of the system
em atomic multipole potential energy of the system
ep polarization potential energy of the system
ect charge transfer potential energy of the system
erxf reaction field potential energy of the system
es solvation potential energy of the system
elf metal ligand field potential energy of the system
eg geometric restraint potential energy of the system
ex extra term potential energy of the system

EWALD Module Ewald summation parameters and options

aewald current value of Ewald convergence coefficient

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aeewald Ewald convergence coefficient for electrostatics
apewald Ewald convergence coefficient for polarization
adewald Ewald convergence coefficient for dispersion
boundary Ewald boundary condition; none, tinfoil or vacuum

EXPOL Module exch-polarization in current structure

nexpol total number of exch polarization sites in system

kpep exchange polarization spring constant at each site
prepep exchange polarization prefactor at each site
dmppep exchange polarization damping alpha at each site
polscale scale matrix for use in exchange polarization
polinv scale matrix inverse for exchange polarization
lpep flag to use exchange polarization at each site

EXTFLD Module applied external electric field vector

exfld components of applied external electric field

use_exfld flag to include applied external electric field

FACES Module Connolly area and volume variables

maxcls maximum number of neighboring atom pairs

maxtt maximum number of temporary tori
maxt maximum number of total tori
maxp maximum number of probe positions
maxv maximum number of vertices
maxen maximum number of concave edges
maxfn maximum number of concave faces
maxc maximum number of circles
maxeq maximum number of convex edges
maxfs maximum number of saddle faces
maxfq maximum number of convex faces
maxcy maximum number of cycles
mxcyeq maximum number of convex edge cycles
mxfqcy maximum number of convex face cycles
na number of atoms
pr probe radius
ar atomic radii
axyz atomic coordinates
skip if true, atom is not used
nosurf if true, atom has no free surface
afree atom free of neighbors
abur atom buried
cls atom numbers of neighbors
clst pointer from neighbor to torus
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acls begin and end pointers for atoms neighbors
ntt number of temporary tori
ttfe first edge of each temporary torus
ttle last edge of each temporary torus
enext pointer to next edge of temporary torus
tta temporary torus atom numbers
ttbur temporary torus buried
ttfree temporary torus free
nt number of tori
tfe torus first edge
ta torus atom numbers
tr torus radius
t torus center
tax torus axis
tfree torus free of neighbors
np number of probe positions
pa probe position atom numbers
p probe position coordinates
nv number of vertices
va vertex atom number
vp vertex probe number
vxyz vertex coordinates
nen number of concave edges
nfn number of concave faces
env vertex numbers for each concave edge
fnen concave face concave edge numbers
nc number of circles
ca circle atom number
ct circle torus number
cr circle radius
c circle center
neq number of convex edges
eqc convex edge circle number
eqv convex edge vertex numbers
afe first convex edge of each atom
ale last convex edge of each atom
eqnext pointer to next convex edge of atom
nfs number of saddle faces
fsen saddle face concave edge numbers
fseq saddle face convex edge numbers
ncy number of cycles
cyneq number of convex edges in cycle
cyeq cycle convex edge numbers
nfq number of convex faces
fqa atom number of convex face
fqncy number of cycles bounding convex face
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fqcy convex face cycle numbers

FFT Module Fast Fourier transform control values

maxprime maximum number of prime factors of FFT dimension

iprime prime factorization of each FFT dimension (FFTPACK)
planf pointer to forward transform data structure (FFTW)
planb pointer to backward transform data structure (FFTW)
ffttable intermediate array used by the FFT routine (FFTPACK)
ffttyp type of FFT package; currently FFTPACK or FFTW

FIELDS Module molecular mechanics force field type

biotyp force field atom type of each biopolymer type

forcefield string used to describe the current forcefield

FILES Module name & number of current structure file

nprior number of previously existing cycle files

ldir length in characters of the directory name
leng length in characters of the base filename
filename fill filename including any extension or version
outfile output filename used for intermediate results

FRACS Module distances to molecular center of mass

xfrac fractional coordinate along a-axis of center of mass

yfrac fractional coordinate along b-axis of center of mass
zfrac fractional coordinate along c-axis of center of mass

FREEZE Module definition of holonomic constraints

nrat number of holonomic distance constraints to apply

nwat4 number of rigid planar four-site water molecules
nratx number of atom group holonomic constraints to apply
iratx group number of group in a holonomic constraint
kratx spatial constraint type (1=plane, 2=line, 3=point)
irat atom numbers of atoms in a holonomic constraint
iwat4 atom numbers involved in rigid four-site waters
rateps convergence tolerance for holonomic constraints
krat ideal distance value for holonomic constraint
kwat4 linear scaling values to build four-site waters
use_rattle logical flag to set use of holonomic contraints
ratimage flag to use minimum image for holonomic constraint

GKSTUF Module generalized Kirkwood solvation values

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gkc tuning parameter exponent in the f(GB) function

gkr generalized Kirkwood cavity radii for atom types

GROUP Module partitioning of system into atom groups

ngrp total number of atom groups in the system

kgrp contiguous list of the atoms in each group
grplist number of the group to which each atom belongs
igrp first and last atom of each group in the list
grpmass total mass of all the atoms in each group
wgrp weight for each set of group-group interactions
use_group flag to use partitioning of system into groups
use_intra flag to include only intragroup interactions
use_inter flag to include only intergroup interactions

HESCUT Module cutoff for Hessian matrix elements

hesscut magnitude of smallest allowed Hessian element

HESSN Module Cartesian Hessian elements for one atom

hessx Hessian elements for x-component of current atom

hessy Hessian elements for y-component of current atom
hessz Hessian elements for z-component of current atom

HPMF Module hydrophobic potential of mean force term

rcarbon radius of a carbon atom for use with HPMF

rwater radius of a water molecule for use with HPMF
acsurf surface area of a hydrophobic carbon atom
safact constant for calculation of atomic surface area
tgrad tanh slope (set very steep, default=100)
toffset shift the tanh plot along the x-axis (default=6)
hpmfcut cutoff distance for pairwise HPMF interactions
hd1 hd2,hd3 hydrophobic PMF well depth parameter
hc1 hc2,hc3 hydrophobic PMF well center point
hw1 hw2,hw3 reciprocal of the hydrophobic PMF well width
npmf number of hydrophobic carbon atoms in the system
ipmf number of the atom for each HPMF carbon atom site
rpmf radius of each atom for use with hydrophobic PMF
acsa SASA value for each hydrophobic PMF carbon atom

IELSCF Module extended Lagrangian induced dipoles

nfree_aux total degrees of freedom for auxiliary dipoles

tautemp_aux time constant for auliliary Berendsen thermostat
kelvin_aux target system temperature for auxiliary dipoles
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uaux auxiliary induced dipole value at each site
upaux auxiliary shadow induced dipoles at each site
vaux auxiliary induced dipole velocity at each site
vpaux auxiliary shadow dipole velocity at each site
aaux auxiliary induced dipole acceleration at each site
apaux auxiliary shadow dipole acceleration at each site
use_ielscf flag to use inertial extended Lagrangian method

IMPROP Module improper dihedrals in current structure

niprop total number of improper dihedral angles in the system

iiprop numbers of the atoms in each improper dihedral angle
kprop force constant values for improper dihedral angles
vprop ideal improper dihedral angle value in degrees

IMPTOR Module improper torsions in current structure

nitors total number of improper torsional angles in the system

iitors numbers of the atoms in each improper torsional angle
itors1 1-fold amplitude and phase for each improper torsion
itors2 2-fold amplitude and phase for each improper torsion
itors3 3-fold amplitude and phase for each improper torsion

INFORM Module program I/O and flow control values

maxask maximum number of queries for interactive input

gpucard integer flag for GPU use (0=no GPU, 1=GPU present)
digits decimal places output for energy and coordinates
iprint steps between status printing (0=no printing)
iwrite steps between coordinate saves (0=no saves)
isend steps between socket communication (0=no sockets)
verbose logical flag to turn on extra information printing
debug logical flag to turn on extensive debug printing
silent logical flag to turn off all information printing
holdup logical flag to wait for carriage return on exit
abort logical flag to stop execution at next chance

INTER Module sum of intermolecular energy components

einter total intermolecular potential energy

IOUNIT Module Fortran input/output unit numbers

input Fortran I/O unit for main input (default=5)

iout Fortran I/O unit for main output (default=6)

KANANG Module angle-angle term forcefield parameters

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anan angle-angle cross term parameters for each atom class

KANGS Module bond angle bend forcefield parameters

maxna maximum number of harmonic angle bend parameter entries

maxna5 maximum number of 5-membered ring angle bend entries
maxna4 maximum number of 4-membered ring angle bend entries
maxna3 maximum number of 3-membered ring angle bend entries
maxnap maximum number of in-plane angle bend parameter entries
maxnaf maximum number of Fourier angle bend parameter entries
acon force constant parameters for harmonic angle bends
acon5 force constant parameters for 5-ring angle bends
acon4 force constant parameters for 4-ring angle bends
acon3 force constant parameters for 3-ring angle bends
aconp force constant parameters for in-plane angle bends
aconf force constant parameters for Fourier angle bends
ang bond angle parameters for harmonic angle bends
ang5 bond angle parameters for 5-ring angle bends
ang4 bond angle parameters for 4-ring angle bends
ang3 bond angle parameters for 3-ring angle bends
angp bond angle parameters for in-plane angle bends
angf phase shift angle and periodicity for Fourier bends
ka string of atom classes for harmonic angle bends
ka5 string of atom classes for 5-ring angle bends
ka4 string of atom classes for 4-ring angle bends
ka3 string of atom classes for 3-ring angle bends
kap string of atom classes for in-plane angle bends
kaf string of atom classes for Fourier angle bends

KANTOR Module angle-torsion forcefield parameters

maxnat maximum number of angle-torsion parameter entries

atcon torsional amplitude parameters for angle-torsion
kat string of atom classes for angle-torsion terms

KATOMS Module atom definition forcefield parameters

atmcls atom class number for each of the atom types

atmnum atomic number for each of the atom types
ligand number of atoms to be attached to each atom type
weight average atomic mass of each atom type
symbol modified atomic symbol for each atom type
describe string identifying each of the atom types

KBONDS Module bond stretching forcefield parameters

maxnb maximum number of bond stretch parameter entries

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maxnb5 maximum number of 5-membered ring bond stretch entries
maxnb4 maximum number of 4-membered ring bond stretch entries
maxnb3 maximum number of 3-membered ring bond stretch entries
maxnel maximum number of electronegativity bond corrections
bcon force constant parameters for harmonic bond stretch
bcon5 force constant parameters for 5-ring bond stretch
bcon4 force constant parameters for 4-ring bond stretch
bcon3 force constant parameters for 3-ring bond stretch
blen bond length parameters for harmonic bond stretch
blen5 bond length parameters for 5-ring bond stretch
blen4 bond length parameters for 4-ring bond stretch
blen3 bond length parameters for 3-ring bond stretch
dlen electronegativity bond length correction parameters
kb string of atom classes for harmonic bond stretch
kb5 string of atom classes for 5-ring bond stretch
kb4 string of atom classes for 4-ring bond stretch
kb3 string of atom classes for 3-ring bond stretch
kel string of atom classes for electronegativity corrections

KCHRGE Module partial charge forcefield parameters

chg partial charge parameters for each atom type

KCPEN Module charge penetration forcefield parameters

cpele valence electron magnitude for each atom class

cpalp alpha charge penetration parameter for each atom class

KCTRN Module charge transfer forcefield parameters

ctchg charge transfer magnitude for each atom class

ctdmp alpha charge transfer parameter for each atom class

KDIPOL Module bond dipole forcefield parameters

maxnd maximum number of bond dipole parameter entries

maxnd5 maximum number of 5-membered ring dipole entries
maxnd4 maximum number of 4-membered ring dipole entries
maxnd3 maximum number of 3-membered ring dipole entries
dpl dipole moment parameters for bond dipoles
dpl5 dipole moment parameters for 5-ring dipoles
dpl4 dipole moment parameters for 4-ring dipoles
dpl3 dipole moment parameters for 3-ring dipoles
pos dipole position parameters for bond dipoles
pos5 dipole position parameters for 5-ring dipoles
pos4 dipole position parameters for 4-ring dipoles
pos3 dipole position parameters for 3-ring dipoles
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kd string of atom classes for bond dipoles
kd5 string of atom classes for 5-ring dipoles
kd4 string of atom classes for 4-ring dipoles
kd3 string of atom classes for 3-ring dipoles

KDSP Module damped dispersion forcefield parameters

dspsix C6 dispersion coefficient for each atom class

dspdmp alpha dispersion parameter for each atom class

KEXPL Module exch-polarization forcefield parameters

pepk exchange-polarization spring constant for atom classes

peppre exchange-polarization prefactor for atom classes
pepdmp exchange-polarization damping alpha for atom classes
pepl exchange-polarization logical flag for atom classes

KEYS Module contents of the keyword control file

maxkey maximum number of lines in the keyword file

nkey number of nonblank lines in the keyword file
keyline contents of each individual keyword file line

KHBOND Module H-bonding term forcefield parameters

maxnhb maximum number of hydrogen bonding pair entries

radhb radius parameter for hydrogen bonding pairs
epshb well depth parameter for hydrogen bonding pairs
khb string of atom types for hydrogen bonding pairs

KIPROP Module improper dihedral forcefield parameters

maxndi maximum number of improper dihedral parameter entries

dcon force constant parameters for improper dihedrals
tdi ideal dihedral angle values for improper dihedrals
kdi string of atom classes for improper dihedral angles

KITORS Module improper torsion forcefield parameters

maxnti maximum number of improper torsion parameter entries

ti1 torsional parameters for improper 1-fold rotation
ti2 torsional parameters for improper 2-fold rotation
ti3 torsional parameters for improper 3-fold rotation
kti string of atom classes for improper torsional parameters

KMULTI Module atomic multipole forcefield parameters

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maxnmp maximum number of atomic multipole parameter entries

multip atomic monopole, dipole and quadrupole values
mpaxis type of local axis definition for atomic multipoles
kmp string of atom types for atomic multipoles

KOPBND Module out-of-plane bend forcefield parameters

maxnopb maximum number of out-of-plane bending entries

opbn force constant parameters for out-of-plane bending
kopb string of atom classes for out-of-plane bending

KOPDST Module out-of-plane distance forcefield params

maxnopd maximum number of out-of-plane distance entries

opds force constant parameters for out-of-plane distance
kopd string of atom classes for out-of-plane distance

KORBS Module pisystem orbital forcefield parameters

maxnpi maximum number of pisystem bond parameter entries

maxnpi5 maximum number of 5-membered ring pibond entries
maxnpi4 maximum number of 4-membered ring pibond entries
sslope slope for bond stretch vs. pi-bond order
sslope5 slope for 5-ring bond stretch vs. pi-bond order
sslope4 slope for 4-ring bond stretch vs. pi-bond order
tslope slope for 2-fold torsion vs. pi-bond order
tslope5 slope for 5-ring 2-fold torsion vs. pi-bond order
tslope4 slope for 4-ring 2-fold torsion vs. pi-bond order
electron number of pi-electrons for each atom class
ionize ionization potential for each atom class
repulse repulsion integral value for each atom class
kpi string of atom classes for pisystem bonds
kpi5 string of atom classes for 5-ring pisystem bonds
kpi4 string of atom classes for 4-ring pisystem bonds

KPITOR Module pi-system torsion forcefield parameters

maxnpt maximum number of pi-system torsion parameter entries

ptcon force constant parameters for pi-system torsions
kpt string of atom classes for pi-system torsion terms

KPOLPR Module special Thole forcefield parameters

maxnpp maximum number of special pair polarization entries

thlpr Thole damping values for special polarization pairs
thdpr Thole direct damping for special polarization pairs
kppr string of atom types for special polarization pairs

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KPOLR Module polarizability forcefield parameters

pgrp connected types in polarization group of each atom type

polr dipole polarizability parameters for each atom type
athl Thole polarizability damping value for each atom type
dthl alternate Thole direct polarization damping values

KREPL Module Pauli repulsion forcefield parameters

prsiz Pauli repulsion size value for each atom class

prdmp alpha Pauli repulsion parameter for each atom class
prele number of valence electrons for each atom class

KSOLUT Module solvation term forcefield parameters

pbr Poisson-Boltzmann radius value for each atom type

csr ddCOSMO solvation radius value for each atom type
gkr Generalized Kirkwood radius value for each atom type
snk neck correction scale factor for each atom type

KSTBND Module stretch-bend forcefield parameters

maxnsb maximum number of stretch-bend parameter entries

stbn force constant parameters for stretch-bend terms
ksb string of atom classes for stretch-bend terms

KSTTOR Module stretch-torsion forcefield parameters

maxnbt maximum number of stretch-torsion parameter entries

btcon torsional amplitude parameters for stretch-torsion
kbt string of atom classes for stretch-torsion terms

KTORSN Module torsional angle forcefield parameters

maxnt maximum number of torsional angle parameter entries

maxnt5 maximum number of 5-membered ring torsion entries
maxnt4 maximum number of 4-membered ring torsion entries
t1 torsional parameters for standard 1-fold rotation
t2 torsional parameters for standard 2-fold rotation
t3 torsional parameters for standard 3-fold rotation
t4 torsional parameters for standard 4-fold rotation
t5 torsional parameters for standard 5-fold rotation
t6 torsional parameters for standard 6-fold rotation
t15 torsional parameters for 1-fold rotation in 5-ring
t25 torsional parameters for 2-fold rotation in 5-ring
t35 torsional parameters for 3-fold rotation in 5-ring
t45 torsional parameters for 4-fold rotation in 5-ring
t55 torsional parameters for 5-fold rotation in 5-ring
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t65 torsional parameters for 6-fold rotation in 5-ring
t14 torsional parameters for 1-fold rotation in 4-ring
t24 torsional parameters for 2-fold rotation in 4-ring
t34 torsional parameters for 3-fold rotation in 4-ring
t44 torsional parameters for 4-fold rotation in 4-ring
t54 torsional parameters for 5-fold rotation in 4-ring
t64 torsional parameters for 6-fold rotation in 4-ring
kt string of atom classes for torsional angles
kt5 string of atom classes for 5-ring torsions
kt4 string of atom classes for 4-ring torsions

KTRTOR Module torsion-torsion forcefield parameters

maxntt maximum number of torsion-torsion parameter entries

maxtgrd maximum dimension of torsion-torsion spline grid
maxtgrd2 maximum number of torsion-torsion spline grid points
tnx number of columns in torsion-torsion spline grid
tny number of rows in torsion-torsion spline grid
ttx angle values for first torsion of spline grid
tty angle values for second torsion of spline grid
tbf function values at points on spline grid
tbx gradient over first torsion of spline grid
tby gradient over second torsion of spline grid
tbxy Hessian cross components over spline grid
ktt string of torsion-torsion atom classes

KURYBR Module Urey-Bradley term forcefield parameters

maxnu maximum number of Urey-Bradley parameter entries

ucon force constant parameters for Urey-Bradley terms
dst13 ideal 1-3 distance parameters for Urey-Bradley terms
ku string of atom classes for Urey-Bradley terms

KVDWPR Module special pair vdw forcefield parameters

maxnvp maximum number of special van der Waals pair entries

radpr radius parameter for special van der Waals pairs
epspr well depth parameter for special van der Waals pairs
kvpr string of atom classes for special van der Waals pairs

KVDWS Module van der Waals term forcefield parameters

rad van der Waals radius parameter for each atom class
eps van der Waals well depth parameter for each atom class
rad4 van der Waals radius parameter in 1-4 interactions
eps4 van der Waals well depth parameter in 1-4 interactions
reduct van der Waals reduction factor for each atom class

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LIGHT Module method of lights pair neighbors indices

nlight total number of sites for method of lights calculation

kbx low index of neighbors of each site in the x-sorted list
kby low index of neighbors of each site in the y-sorted list
kbz low index of neighbors of each site in the z-sorted list
kex high index of neighbors of each site in the x-sorted list
key high index of neighbors of each site in the y-sorted list
kez high index of neighbors of each site in the z-sorted list
locx maps the x-sorted list into original interaction list
locy maps the y-sorted list into original interaction list
locz maps the z-sorted list into original interaction list
rgx maps the original interaction list into x-sorted list
rgy maps the original interaction list into y-sorted list
rgz maps the original interaction list into z-sorted list

LIMITS Module interaction taper & cutoff distances

vdwcut cutoff distance for van der Waals interactions

repcut cutoff distance for Pauli repulsion interactions
dispcut cutoff distance for dispersion interactions
chgcut cutoff distance for charge-charge interactions
dplcut cutoff distance for dipole-dipole interactions
mpolecut cutoff distance for atomic multipole interactions
ctrncut cutoff distance for charge transfer interactions
vdwtaper distance at which van der Waals switching begins
reptaper distance at which Pauli repulsion switching begins
disptaper distance at which dispersion switching begins
chgtaper distance at which charge-charge switching begins
dpltaper distance at which dipole-dipole switching begins
mpoletaper distance at which atomic multipole switching begins
ctrntaper distance at which charge transfer switching begins
ewaldcut cutoff distance for real space Ewald electrostatics
dewaldcut cutoff distance for real space Ewald dispersion
usolvcut cutoff distance for dipole solver preconditioner
use_ewald logical flag governing use of electrostatic Ewald
use_dewald logical flag governing use of dispersion Ewald
use_lights logical flag governing use of method of lights
use_list logical flag governing use of any neighbor lists
use_vlist logical flag governing use of van der Waals list
use_dlist logical flag governing use of dispersion list
use_clist logical flag governing use of charge list
use_mlist logical flag governing use of multipole list
use_ulist logical flag governing use of preconditioner list

LINMIN Module line search minimization parameters

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intmax maximum number of interpolations during line search

stpmin minimum step length in current line search direction
stpmax maximum step length in current line search direction
cappa stringency of line search (0=tight < cappa < 1=loose)
slpmax projected gradient above which stepsize is reduced
angmax maximum angle between search direction and -gradient

MATH Module mathematical and geometrical constants

pi numerical value of the geometric constant

elog numerical value of the natural logarithm base
radian conversion factor from radians to degrees
logten numerical value of the natural log of ten
twosix numerical value of the sixth root of two
sqrtpi numerical value of the square root of Pi
sqrttwo numerical value of the square root of two
sqrtthree numerical value of the square root of three

MDSTUF Module molecular dynamics trajectory controls

nfree total number of degrees of freedom for a system

irest steps between removal of COM motion (0=no removal)
bmnmix mixing coefficient for use with Beeman integrator
nrespa inner steps per outer step for RESPA integrator
arespa inner time step for use with RESPA integrator
dorest logical flag to remove center of mass motion
integrate type of molecular dynamics integration algorithm

MERCK Module MMFF-specific force field parameters

nlignes number of atom pairs having MMFF Bond Type 1

bt_1 atom pairs having MMFF Bond Type 1
eqclass table of atom class equivalencies used to find
default parameters if explicit values are missing
see J. Comput. Chem., 17, 490-519, '95, Table IV)
crd number of attached neighbors |
val valency value | see T. A. Halgren,
pilp if 0, no lone pair | J. Comput. Chem.,
if 1, one or more lone pair(s) | 17, 616-645 (1995)
mltb multibond indicator |
arom aromaticity indicator |
lin linearity indicator |
sbmb single- vs multiple-bond flag |
mmffarom aromatic rings parameters
mmffaromc cationic aromatic rings parameters
mmffaroma anionic aromatic rings parameters

MINIMA Module general parameters for minimizations

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nextiter iteration number to use for the first iteration

fctmin value below which function is deemed optimized
hguess initial value for the H-matrix diagonal elements
maxiter maximum number of iterations during optimization

MOLCUL Module individual molecules in current system

nmol total number of separate molecules in the system

imol first and last atom of each molecule in the list
kmol contiguous list of the atoms in each molecule
molcule number of the molecule to which each atom belongs
totmass total weight of all the molecules in the system
molmass molecular weight for each molecule in the system

MOLDYN Module MD trajectory velocity & acceleration

v current velocity of each atom along the x,y,z-axes

a current acceleration of each atom along x,y,z-axes
aalt alternate acceleration of each atom along x,y,z-axes

MOMENT Module electric multipole moment components

netchg net electric charge for the total system

netdpl dipole moment magnitude for the total system
netqdp diagonal quadrupole (Qxx, Qyy, Qzz) for system
xdpl dipole vector x-component in the global frame
ydpl dipole vector y-component in the global frame
zdpl dipole vector z-component in the global frame
xxqdp quadrupole tensor xx-component in global frame
xyqdp quadrupole tensor xy-component in global frame
xzqdp quadrupole tensor xz-component in global frame
yxqdp quadrupole tensor yx-component in global frame
yyqdp quadrupole tensor yy-component in global frame
yzqdp quadrupole tensor yz-component in global frame
zxqdp quadrupole tensor zx-component in global frame
zyqdp quadrupole tensor zy-component in global frame
zzqdp quadrupole tensor zz-component in global frame

MPLPOT Module multipole functional form details

m2scale scale factor for 1-2 multipole energy interactions

m3scale scale factor for 1-3 multipole energy interactions
m4scale scale factor for 1-4 multipole energy interactions
m5scale scale factor for 1-5 multipole energy interactions
use_chgpen flag to use charge penetration damped potential
pentyp type of penetration damping (NONE, GORDON1, GORDON2)

MPOLE Module atomic multipoles in current structure

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maxpole max components (monopole=1,dipole=4,quadrupole=13)

npole total number of multipole sites in the system
ipole number of the atom for each multipole site
polsiz number of multipole components at each atom
pollist multipole site for each atom (0=no multipole)
zaxis number of the z-axis defining atom for each atom
xaxis number of the x-axis defining atom for each atom
yaxis number of the y-axis defining atom for each atom
pole local frame Cartesian multipoles for each atom
rpole global frame Cartesian multipoles for each atom
mono0 original atomic monopole values for charge flux
polaxe local coordinate frame type for each atom

MRECIP Module reciprocal PME for permanent multipoles

vmxx scalar sum xx-component of virial due to multipoles

vmyy scalar sum yy-component of virial due to multipoles
vmzz scalar sum zz-component of virial due to multipoles
vmxy scalar sum xy-component of virial due to multipoles
vmxz scalar sum xz-component of virial due to multipoles
vmyz scalar sum yz-component of virial due to multipoles
cmp Cartesian permenent multipoles as polytensor vector
fmp fractional permanent multipoles as polytensor vector
cphi Cartesian permanent multipole potential and field
fphi fractional permanent multipole potential and field

MUTANT Module free energy calculation hybrid atoms

nmut number of atoms mutated from initial to final state

vcouple van der Waals lambda type (0=decouple, 1=annihilate)
imut atomic sites differing in initial and final state
type0 atom type of each atom in the initial state system
class0 atom class of each atom in the initial state system
type1 atom type of each atom in the final state system
class1 atom class of each atom in the final state system
lambda generic weighting between initial and final states
vlambda state weighting value for van der Waals potentials
elambda state weighting value for electrostatic potentials
tlambda state weighting value for torsional potential
scexp scale factor for soft core buffered 14-7 potential
scalpha scale factor for soft core buffered 14-7 potential
mut true if an atom is to be mutated, false otherwise

NEIGH Module pairwise neighbor list indices & storage

maxvlst maximum size of van der Waals pair neighbor lists

maxelst maximum size of electrostatic pair neighbor lists
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maxulst maximum size of dipole preconditioner pair lists
nvlst number of sites in list for each vdw site
vlst site numbers in neighbor list of each vdw site
nelst number of sites in list for each electrostatic site
elst site numbers in list of each electrostatic site
nulst number of sites in list for each preconditioner site
ulst site numbers in list of each preconditioner site
lbuffer width of the neighbor list buffer region
pbuffer width of the preconditioner list buffer region
lbuf2 square of half the neighbor list buffer width
pbuf2 square of half the preconditioner list buffer width
vbuf2 square of van der Waals cutoff plus the list buffer
vbufx square of van der Waals cutoff plus 2X list buffer
dbuf2 square of dispersion cutoff plus the list buffer
dbufx square of dispersion cutoff plus 2X list buffer
cbuf2 square of charge cutoff plus the list buffer
cbufx square of charge cutoff plus 2X list buffer
mbuf2 square of multipole cutoff plus the list buffer
mbufx square of multipole cutoff plus 2X list buffer
ubuf2 square of preconditioner cutoff plus the list buffer
ubufx square of preconditioner cutoff plus 2X list buffer
xvold x-coordinate at last vdw/dispersion list update
yvold y-coordinate at last vdw/dispersion list update
zvold z-coordinate at last vdw/dispersion list update
xeold x-coordinate at last electrostatic list update
yeold y-coordinate at last electrostatic list update
zeold z-coordinate at last electrostatic list update
xuold x-coordinate at last preconditioner list update
yuold y-coordinate at last preconditioner list update
zuold z-coordinate at last preconditioner list update
dovlst logical flag to rebuild vdw neighbor list
dodlst logical flag to rebuild dispersion neighbor list
doclst logical flag to rebuild charge neighbor list
domlst logical flag to rebuild multipole neighbor list
doulst logical flag to rebuild preconditioner neighbor list

NONPOL Module nonpolar cavity & dispersion parameters

epso water oxygen eps for implicit dispersion term

epsh water hydrogen eps for implicit dispersion term
rmino water oxygen Rmin for implicit dispersion term
rminh water hydrogen Rmin for implicit dispersion term
awater water number density at standard temp & pressure
slevy enthalpy-to-free energy scale factor for dispersion
shctd HCT overlap scale factor for the dispersion integral
dspoff radius offset for the start of dispersion integral
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cavprb probe radius for use in computing cavitation energy
solvprs limiting microscopic solvent pressure value
surften limiting macroscopic surface tension value
spcut starting radius for solvent pressure tapering
spoff cutoff radius for solvent pressure tapering
stcut starting radius for surface tension tapering
stoff cutoff radius for surface tension tapering
radcav atomic radius of each atom for cavitation energy
raddsp atomic radius of each atom for dispersion energy
epsdsp vdw well depth of each atom for dispersion energy
cdisp maximum dispersion energy for each atom

NUCLEO Module parameters for nucleic acid structure

pucker sugar pucker, either 2=2'-endo or 3=3'-endo

glyco glycosidic torsional angle for each nucleotide
bkbone phosphate backbone angles for each nucleotide
dblhlx flag to mark system as nucleic acid double helix
deoxy flag to mark deoxyribose or ribose sugar units
hlxform helix form (A, B or Z) of polynucleotide strands

OMEGA Module torsional space dihedral angle values

nomega number of dihedral angles allowed to rotate

iomega numbers of two atoms defining rotation axis
zline line number in Z-matrix of each dihedral angle
dihed current value in radians of each dihedral angle

OPBEND Module out-of-plane bends in current structure

nopbend total number of out-of-plane bends in the system

iopb bond angle numbers used in out-of-plane bending
opbk force constant values for out-of-plane bending

OPDIST Module out-of-plane distances in structure

nopdist total number of out-of-plane distances in the system

iopd numbers of the atoms in each out-of-plane distance
opdk force constant values for out-of-plane distance

OPENMP Module OpenMP processor and thread values

nproc number of processors available to OpenMP

nthread number of threads to be used with OpenMP

ORBITS Module conjugated pisystem orbital energies

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qorb number of pi-electrons contributed by each atom

worb ionization potential of each pisystem atom
emorb repulsion integral for each pisystem atom

OUTPUT Module output file format control parameters

archive logical flag for coordinates in Tinker XYZ format

binary logical flag for coordinates in DCD binary format
noversion logical flag governing use of filename versions
overwrite logical flag to overwrite intermediate files inplace
arcsave logical flag to save coordinates in Tinker XYZ format
dcdsave logical flag to save coordinates in DCD binary format
cyclesave logical flag to mark use of numbered cycle files
velsave logical flag to save velocity vector components
frcsave logical flag to save force vector components
uindsave logical flag to save induced atomic dipoles
coordtype selects Cartesian, internal, rigid body or none

PARAMS Module force field parameter file contents

maxprm maximum number of lines in the parameter file

nprm number of nonblank lines in the parameter file
prmline contents of each individual parameter file line

PATHS Module Elber reaction path method parameters

pnorm length of the reactant-product vector

acoeff transformation matrix 'A' from Elber algorithm
pc0 reactant Cartesian coordinates as variables
pc1 product Cartesian coordinates as variables
pvect vector connecting the reactant and product
pstep step per cycle along reactant-product vector
pzet current projection on reactant-product vector
gc gradient of the path constraints

PBSTUF Module Poisson-Boltzmann solvation parameters

APBS configuration parameters (see APBS documentation for details). In the column on the right
are possible values for each variable, with default values given in brackets. Only a subset of the
APBS options are supported and/or are appropriate for use with AMOEBA.

pbtyp lpbe
pbsoln mg-auto, [mg-manual]
bcfl boundary conditions zero, sdh, [mdh]
chgm multipole discretization spl4
srfm surface method mol, smol, [spl4]
dime number of grid points [65, 65, 65]
grid grid spacing (mg-manual) fxn of "dime"
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cgrid coarse grid spacing fxn of "dime"
fgrid fine grid spacing cgrid / 2
gcent grid center (mg-manual) center of mass
cgcent coarse grid center center of mass
fgcent fine grid center center of mass
pdie solute/homogeneous dieletric [1.0]
sdie solvent dieletric [78.3]
ionn number of ion species [0]
ionc ion concentration (M) [0.0]
ionq ion charge (electrons) [1.0]
ionr ion radius (A) [2.0]
srad solvent probe radius (A) [1.4]
swin surface spline window width [0.3]
sdens density of surface points [10.0]
smin minimum distance between an [10.0]
pbe Poisson-Boltzmann permanent multipole solvation energy
apbe Poisson-Boltzmann permanent multipole energy over atoms
pbr Poisson-Boltzmann cavity radii for atom types
pbep Poisson-Boltzmann energies on permanent multipoles
pbfp Poisson-Boltzmann forces on permanent multipoles
pbtp Poisson-Boltzmann torques on permanent multipoles
pbeuind Poisson-Boltzmann field due to induced dipoles
pbeuinp Poisson-Boltzmann field due to non-local induced dipoles

PDB Module Protein Data Bank structure definition

npdb number of atoms stored in Protein Data Bank format

nres number of residues stored in Protein Data Bank format
resnum number of the residue to which each atom belongs
resatm number of first and last atom in each residue
npdb12 number of atoms directly bonded to each CONECT atom
ipdb12 atom numbers of atoms connected to each CONECT atom
pdblist list of the Protein Data Bank atom number of each atom
xpdb x-coordinate of each atom stored in PDB format
ypdb y-coordinate of each atom stored in PDB format
zpdb z-coordinate of each atom stored in PDB format
altsym string with PDB alternate locations to be included
pdbres Protein Data Bank residue name assigned to each atom
pdbatm Protein Data Bank atom name assigned to each atom
pdbtyp Protein Data Bank record type assigned to each atom
chnsym string with PDB chain identifiers to be included
instyp string with PDB insertion records to be included

PHIPSI Module phi-psi-omega-chi angles for protein

chiral chirality of each amino acid residue (1=L, -1=D)

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disulf residue joined to each residue via a disulfide link
phi value of the phi angle for each amino acid residue
psi value of the psi angle for each amino acid residue
omg value of the omega angle for each amino acid residue
chi values of the chi angles for each amino acid residue

PIORBS Module conjugated system in current structure

norbit total number of pisystem orbitals in the system

nconj total number of separate conjugated piystems
reorbit number of evaluations between orbital updates
nbpi total number of bonds affected by the pisystem
ntpi total number of torsions affected by the pisystem
iorbit numbers of the atoms containing pisystem orbitals
iconj first and last atom of each pisystem in the list
kconj contiguous list of atoms in each pisystem
piperp atoms defining a normal plane to each orbital
ibpi bond and piatom numbers for each pisystem bond
itpi torsion and pibond numbers for each pisystem torsion
pbpl pi-bond orders for bonds in "planar" pisystem
pnpl pi-bond orders for bonds in "nonplanar" pisystem
listpi atom list indicating whether each atom has an orbital

PISTUF Module bond order-related pisystem parameters

bkpi bond stretch force constants for pi-bond order of 1.0

blpi ideal bond length values for a pi-bond order of 1.0
kslope rate of force constant decrease with bond order decrease
lslope rate of bond length increase with a bond order decrease
torsp2 2-fold torsional energy barrier for pi-bond order of 1.0

PITORS Module pi-system torsions in current structure

npitors total number of pi-system torsional interactions

ipit numbers of the atoms in each pi-system torsion
kpit 2-fold pi-system torsional force constants

PME Module values for particle mesh Ewald summation

nfft1 current number of PME grid points along a-axis

nfft2 current number of PME grid points along b-axis
nfft3 current number of PME grid points along c-axis
nefft1 number of grid points along electrostatic a-axis
nefft2 number of grid points along electrostatic b-axis
nefft3 number of grid points along electrostatic c-axis
ndfft1 number of grid points along dispersion a-axis
ndfft2 number of grid points along dispersion b-axis
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ndfft3 number of grid points along dispersion c-axis
bsorder current order of the PME B-spline values
bseorder order of the electrostatic PME B-spline values
bsporder order of the polarization PME B-spline values
bsdorder order of the dispersion PME B-spline values
igrid initial Ewald grid values for B-spline
bsmod1 B-spline moduli along the a-axis direction
bsmod2 B-spline moduli along the b-axis direction
bsmod3 B-spline moduli along the c-axis direction
bsbuild B-spline derivative coefficient temporary storage
thetai1 B-spline coefficients along the a-axis
thetai2 B-spline coefficients along the b-axis
thetai3 B-spline coefficients along the c-axis
qgrid values on the particle mesh Ewald grid
qfac prefactors for the particle mesh Ewald grid

POLAR Module induced dipole moments & polarizability

npolar total number of polarizable sites in the system

ipolar number of the atom for each polarizable site
jpolar index into polarization parameter matrix for each atom
polarity dipole polarizability for each atom site (Ang**3)
thole Thole polarization damping value for each atom
tholed Thole direct polarization damping value for each atom
pdamp value of polarizability scale factor for each atom
thlval Thole damping parameter value for each atom type pair
thdval alternate Thole direct damping value for atom type pair
udir direct induced dipole components for each atom site
udirp direct induced dipoles in field used for energy terms
udirs direct GK or PB induced dipoles for each atom site
udirps direct induced dipoles in field used for GK or PB energy
uind mutual induced dipole components for each atom site
uinp mutual induced dipoles in field used for energy terms
uinds mutual GK or PB induced dipoles for each atom site
uinps mutual induced dipoles in field used for GK or PB energy
uexact exact SCF induced dipoles to full numerical precision
douind flag to allow induced dipoles at each atom site

POLGRP Module polarization group connectivity lists

maxp11 maximum number of atoms in a polarization group

maxp12 maximum number of atoms in groups 1-2 to an atom
maxp13 maximum number of atoms in groups 1-3 to an atom
maxp14 maximum number of atoms in groups 1-4 to an atom
np11 number of atoms in polarization group of each atom
np12 number of atoms in groups 1-2 to each atom
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np13 number of atoms in groups 1-3 to each atom
np14 number of atoms in groups 1-4 to each atom
ip11 atom numbers of atoms in same group as each atom
ip12 atom numbers of atoms in groups 1-2 to each atom
ip13 atom numbers of atoms in groups 1-3 to each atom
ip14 atom numbers of atoms in groups 1-4 to each atom

POLOPT Module induced dipoles for OPT extrapolation

maxopt maximum order for OPT induced dipole extrapolation

optorder highest coefficient order for OPT dipole extrapolation
optlevel current OPT order for reciprocal potential and field
copt coefficients for OPT total induced dipole moments
copm coefficients for OPT incremental induced dipole moments
uopt OPT induced dipole components at each multipole site
uoptp OPT induced dipoles in field used for energy terms
uopts OPT GK or PB induced dipoles at each multipole site
uoptps OPT induced dipoles in field used for GK or PB energy
fopt OPT fractional reciprocal potentials at multipole sites
foptp OPT fractional reciprocal potentials for energy terms

POLPCG Module induced dipoles via the PCG solver

mindex index into preconditioner inverse for PCG solver

pcgpeek value of acceleration factor for PCG peek step
minv preconditioner inverse for induced dipole PCG solver
pcgprec flag to allow use of preconditioner with PCG solver
pcgguess flag to use initial PCG based on direct field

POLPOT Module polarization functional form details

politer maximum number of induced dipole SCF iterations

poleps induced dipole convergence criterion (rms Debye/atom)
p2scale scale factor for 1-2 polarization energy interactions
p3scale scale factor for 1-3 polarization energy interactions
p4scale scale factor for 1-4 polarization energy interactions
p5scale scale factor for 1-5 polarization energy interactions
p2iscale scale factor for 1-2 intragroup polarization energy
p3iscale scale factor for 1-3 intragroup polarization energy
p4iscale scale factor for 1-4 intragroup polarization energy
p5iscale scale factor for 1-5 intragroup polarization energy
d1scale scale factor for intra-group direct induction
d2scale scale factor for 1-2 group direct induction
d3scale scale factor for 1-3 group direct induction
d4scale scale factor for 1-4 group direct induction
u1scale scale factor for intra-group mutual induction
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u2scale scale factor for 1-2 group mutual induction
u3scale scale factor for 1-3 group mutual induction
u4scale scale factor for 1-4 group mutual induction
w2scale scale factor for 1-2 induced dipole interactions
w3scale scale factor for 1-3 induced dipole interactions
w4scale scale factor for 1-4 induced dipole interactions
w5scale scale factor for 1-5 induced dipole interactions
udiag acceleration factor for induced dipole SCF iterations
dpequal flag to set dscale values equal to pscale values
use_thole flag to use Thole damped polarization interactions
use_tholed flag to use alternate Thole for direct polarization
use_expol flag to use damped exchange polarization correction
poltyp type of polarization (MUTUAL, DIRECT, OPT or TCG)

POLTCG Module induced dipoles via the TCG solver

tcgorder total number of TCG iterations to be used

tcgnab number of mutual induced dipole components
tcgpeek value of acceleration factor for TCG peek step
uad left-hand side mutual induced d-dipoles
uap left-hand side mutual induced p-dipoles
ubd right-hand side mutual induced d-dipoles
ubp right-hand side mutual induced p-dipoles
tcgguess flag to use initial TCG based on direct field

POTENT Module usage of potential energy components

use_bond logical flag governing use of bond stretch potential

use_angle logical flag governing use of angle bend potential
use_strbnd logical flag governing use of stretch-bend potential
use_urey logical flag governing use of Urey-Bradley potential
use_angang logical flag governing use of angle-angle cross term
use_opbend logical flag governing use of out-of-plane bend term
use_opdist logical flag governing use of out-of-plane distance
use_improp logical flag governing use of improper dihedral term
use_imptor logical flag governing use of improper torsion term
use_tors logical flag governing use of torsional potential
use_pitors logical flag governing use of pi-system torsion term
use_strtor logical flag governing use of stretch-torsion term
use_angtor logical flag governing use of angle-torsion term
use_tortor logical flag governing use of torsion-torsion term
use_vdw logical flag governing use of van der Waals potential
use_repel logical flag governing use of Pauli repulsion term
use_disp logical flag governing use of dispersion potential
use_charge logical flag governing use of charge-charge potential
use_chgdpl logical flag governing use of charge-dipole potential
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use_dipole logical flag governing use of dipole-dipole potential
use_mpole logical flag governing use of multipole potential
use_polar logical flag governing use of polarization term
use_chgtrn logical flag governing use of charge transfer term
use_chgflx logical flag governing use of charge flux term
use_rxnfld logical flag governing use of reaction field term
use_solv logical flag governing use of continuum solvation term
use_metal logical flag governing use of ligand field term
use_geom logical flag governing use of geometric restraints
use_extra logical flag governing use of extra potential term
use_born logical flag governing use of Born radii values
use_orbit logical flag governing use of pisystem computation
use_mutate logical flag governing use of hybrid potential terms

POTFIT Module values for electrostatic potential fit

nconf total number of configurations to be analyzed

namax maximum number of atoms in the largest configuration
ngatm total number of atoms with active potential grid points
nfatm total number of atoms in electrostatic potential fit
npgrid total number of electrostatic potential grid points
ipgrid atom associated with each potential grid point
resp weight used to restrain parameters to original values
xdpl0 target x-component of molecular dipole moment
ydpl0 target y-component of molecular dipole moment
zdpl0 target z-component of molecular dipole moment
xxqdp0 target xx-component of molecular quadrupole moment
xyqdp0 target xy-component of molecular quadrupole moment
xzqdp0 target xz-component of molecular quadrupole moment
yyqdp0 target yy-component of molecular quadrupole moment
yzqdp0 target yz-component of molecular quadrupole moment
zzqdp0 target zz-component of molecular quadrupole moment
fit0 initial value of each parameter used in potential fit
fchg partial charges by atom type during potential fit
fpol atomic multipoles by atom type during potential fit
pgrid Cartesian coordinates of potential grid points
epot values of electrostatic potential at grid points
use_dpl flag to include molecular dipole in potential fit
use_qdp flag to include molecular quadrupole in potential fit
fit_mpl flag for atomic monopoles to vary in potential fit
fit_dpl flag for atomic dipoles to vary in potential fit
fit_qdp flag for atomic quadrupoles to vary in potential fit
fit_chgpen flag for charge penetration to vary in potential fit
fitchg flag marking atom types used in partial charge fit
fitpol flag marking atom types used in atomic multipole fit
fitcpen flag marking atom types used in charge penetration
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gatm flag to use potential grid points around each atom
fatm flag to use each atom in electrostatic potential fit
vchg flag for partial charge at each atom in fitting
vpol flag for atomic multipoles at each atom in fitting
vcpen flag for charge penetration at each atom in fitting
resptyp electrostatic restraint target (ORIG, ZERO or NONE)
varpot descriptive name for each variable in potential fit

PTABLE Module symbols and info for chemical elements

maxele maximum number of elements from periodic table

atmass standard atomic weight for each chemical element
vdwrad van der Waals radius for each chemical element
covrad covalent radius for each chemical element
elemnt atomic symbol for each chemical element

REFER Module reference atomic coordinate storage

nref total number of atoms in each reference system

refltitle length in characters of reference title lines
refleng length in characters of reference base filenames
reftyp atom types of the atoms in each reference system
n12ref number of atoms bonded to each reference atom
i12ref atom numbers of atoms 1-2 connected to each atom
xboxref reference a-axis length of periodic box
yboxref reference b-axis length of periodic box
zboxref reference c-axis length of periodic box
alpharef reference angle between b- and c-axes of box
betaref reference angle between a- and c-axes of box
gammaref reference angle between a- and b-axes of box
xref reference x-coordinates for atoms in each system
yref reference y-coordinates for atoms in each system
zref reference z-coordinates for atoms in each system
refnam atom names of the atoms in each reference system
reffile full filename for each reference system
reftitle title used to describe each reference system

REPEL Module Pauli repulsion for current structure

nrep total number of repulsion sites in the system

irep number of the atom for each repulsion site
replist repulsion multipole site for each atom (0=none)
sizpr Pauli repulsion size parameter value for each atom
dmppr Pauli repulsion alpha damping value for each atom
elepr Pauli repulsion valence electrons for each atom
repole repulsion Cartesian multipoles in the local frame
rrepole repulsion Cartesian multipoles in the global frame

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REPPOT Module repulsion interaction scale factors

r2scale scale factor for 1-2 repulsion energy interactions

r3scale scale factor for 1-3 repulsion energy interactions
r4scale scale factor for 1-4 repulsion energy interactions
r5scale scale factor for 1-5 repulsion energy interactions

RESDUE Module amino acid & nucleotide residue names

maxamino maximum number of amino acid residue types

maxnuc maximum number of nucleic acid residue types
ntyp biotypes for mid-chain peptide backbone N atoms
catyp biotypes for mid-chain peptide backbone CA atoms
ctyp biotypes for mid-chain peptide backbone C atoms
hntyp biotypes for mid-chain peptide backbone HN atoms
otyp biotypes for mid-chain peptide backbone O atoms
hatyp biotypes for mid-chain peptide backbone HA atoms
cbtyp biotypes for mid-chain peptide backbone CB atoms
nntyp biotypes for N-terminal peptide backbone N atoms
cantyp biotypes for N-terminal peptide backbone CA atoms
cntyp biotypes for N-terminal peptide backbone C atoms
hnntyp biotypes for N-terminal peptide backbone HN atoms
ontyp biotypes for N-terminal peptide backbone O atoms
hantyp biotypes for N-terminal peptide backbone HA atoms
nctyp biotypes for C-terminal peptide backbone N atoms
cactyp biotypes for C-terminal peptide backbone CA atoms
cctyp biotypes for C-terminal peptide backbone C atoms
hnctyp biotypes for C-terminal peptide backbone HN atoms
octyp biotypes for C-terminal peptide backbone O atoms
hactyp biotypes for C-terminal peptide backbone HA atoms
o5typ biotypes for nucleotide backbone and sugar O5' atoms
c5typ biotypes for nucleotide backbone and sugar C5' atoms
h51typ biotypes for nucleotide backbone and sugar H5' atoms
h52typ biotypes for nucleotide backbone and sugar H5'' atoms
c4typ biotypes for nucleotide backbone and sugar C4' atoms
h4typ biotypes for nucleotide backbone and sugar H4' atoms
o4typ biotypes for nucleotide backbone and sugar O4' atoms
c1typ biotypes for nucleotide backbone and sugar C1' atoms
h1typ biotypes for nucleotide backbone and sugar H1' atoms
c3typ biotypes for nucleotide backbone and sugar C3' atoms
h3typ biotypes for nucleotide backbone and sugar H3' atoms
c2typ biotypes for nucleotide backbone and sugar C2' atoms
h21typ biotypes for nucleotide backbone and sugar H2' atoms
o2typ biotypes for nucleotide backbone and sugar O2' atoms
h22typ biotypes for nucleotide backbone and sugar H2'' atoms
o3typ biotypes for nucleotide backbone and sugar O3' atoms
ptyp biotypes for nucleotide backbone and sugar P atoms
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optyp biotypes for nucleotide backbone and sugar OP atoms
h5ttyp biotypes for nucleotide backbone and sugar H5T atoms
h3ttyp biotypes for nucleotide backbone and sugar H3T atoms
amino three-letter abbreviations for amino acids types
nuclz three-letter abbreviations for nucleic acids types
amino1 one-letter abbreviations for amino acids types
nuclz1 one-letter abbreviations for nucleic acids types

RESTRN Module parameters for geometrical restraints

npfix number of position restraints to be applied

ndfix number of distance restraints to be applied
nafix number of angle restraints to be applied
ntfix number of torsional restraints to be applied
ngfix number of group distance restraints to be applied
nchir number of chirality restraints to be applied
ipfix atom number involved in each position restraint
kpfix flags to use x-, y-, z-coordinate position restraints
idfix atom numbers defining each distance restraint
iafix atom numbers defining each angle restraint
itfix atom numbers defining each torsional restraint
igfix group numbers defining each group distance restraint
ichir atom numbers defining each chirality restraint
depth depth of shallow Gaussian basin restraint
width exponential width coefficient of Gaussian basin
rwall radius of spherical droplet boundary restraint
xpfix x-coordinate target for each restrained position
ypfix y-coordinate target for each restrained position
zpfix z-coordinate target for each restrained position
pfix force constant and flat-well range for each position
dfix force constant and target range for each distance
afix force constant and target range for each angle
tfix force constant and target range for each torsion
gfix force constant and target range for each group distance
chir force constant and target range for chiral centers
use_basin logical flag governing use of Gaussian basin
use_wall logical flag governing use of droplet boundary

RGDDYN Module rigid body MD velocities and momenta

xcmo x-component from each atom to center of rigid body

ycmo y-component from each atom to center of rigid body
zcmo z-component from each atom to center of rigid body
vcm current translational velocity of each rigid body
wcm current angular velocity of each rigid body
lm current angular momentum of each rigid body
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vc half-step translational velocity for kinetic energy
wc half-step angular velocity for kinetic energy
linear logical flag to mark group as linear or nonlinear

RIGID Module rigid body coordinates for atom groups

xrb rigid body reference x-coordinate for each atom

yrb rigid body reference y-coordinate for each atom
zrb rigid body reference z-coordinate for each atom
rbc current rigid body coordinates for each group
use_rigid flag to mark use of rigid body coordinate system

RING Module number and location of ring structures

nring3 total number of 3-membered rings in the system

nring4 total number of 4-membered rings in the system
nring5 total number of 5-membered rings in the system
nring6 total number of 6-membered rings in the system
nring7 total number of 7-membered rings in the system
iring3 numbers of the atoms involved in each 3-ring
iring4 numbers of the atoms involved in each 4-ring
iring5 numbers of the atoms involved in each 5-ring
iring6 numbers of the atoms involved in each 6-ring
iring7 numbers of the atoms involved in each 7-ring

ROTBND Module molecule partitions for bond rotation

nrot total number of atoms moving when bond rotates

rot atom numbers of atoms moving when bond rotates
use_short logical flag governing use of shortest atom list

RXNFLD Module reaction field matrix and indices

ijk indices into the reaction field element arrays

b1 first reaction field matrix element array
b2 second reaction field matrix element array

RXNPOT Module reaction field functional form details

rfsize radius of reaction field sphere centered at origin

rfbulkd bulk dielectric constant of reaction field continuum
rfterms number of terms to use in reaction field summation

SCALES Module optimization parameter scale factors

scale multiplicative factor for each optimization parameter

set_scale logical flag to show if scale factors have been set

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SEQUEN Module sequence information for biopolymer

nseq total number of residues in biopolymer sequences

nchain number of separate biopolymer sequence chains
ichain first and last residue in each biopolymer chain
seqtyp residue type for each residue in the sequence
seqatm base atom number for each residue (Calpha or C4')
chnnam one-letter identifier for each sequence chain
seq three-letter code for each residue in the sequence
chntyp contents of each chain (GENERIC, PEPTIDE or NUCLEIC)

SHAPES Module UnionBall area and volume variables

maxedge maximum number of edges between ball centers

maxtetra maximum number of tetrahedra in the system
npoint total number of balls (points) in the system
nvertex total number of vertices in the system
ntetra total number of tetrahedra in the system
nnew total number of entries on new tetrahedra list
nfree total number of spaces on free tetrahedra list
nkill total number of tetrahedra on list to kill
nlinkfacet total number of triangle facets in the system
newlist list with index numbers of the new tetrahedra
freespace list of the tetrahedra currently in free space
killspace list of the existing tetrahedra to be killed
vinfo information value for each of the vertices
tedge number of an edge found in each tetrahedron
tinfo orientation information for each tetrahedron
tnindex index related to tetrahedron orientation
tetra numbers of the four balls in each tetrahedron
tneighbor store the four neighbors of each tetrahedron
linkfacet numbers of two tetrahedra defining each facet
linkindex vertex numbers opposite each facet triangle
epsln2 minimal value of determinant over two balls
epsln3 minimal value of determinant over three balls
epsln4 minimal value of determinant over four balls
epsln5 minimal value of determinant over five balls
crdball coordinates in Angstroms of balls as 1-D array
radball radius value for each ball in Angstroms
wghtball weight value assigned for each ball

SHUNT Module polynomial switching function values

off distance at which the potential energy goes to zero

off2 square of distance at which the potential goes to zero
cut distance at which switching of the potential begins
cut2 square of distance at which the switching begins
c0 zeroth order coefficient of multiplicative switch
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c1 first order coefficient of multiplicative switch
c2 second order coefficient of multiplicative switch
c3 third order coefficient of multiplicative switch
c4 fourth order coefficient of multiplicative switch
c5 fifth order coefficient of multiplicative switch
f0 zeroth order coefficient of additive switch function
f1 first order coefficient of additive switch function
f2 second order coefficient of additive switch function
f3 third order coefficient of additive switch function
f4 fourth order coefficient of additive switch function
f5 fifth order coefficient of additive switch function
f6 sixth order coefficient of additive switch function
f7 seventh order coefficient of additive switch function

SIZES Module parameters to set array dimensions

maxatm maximum number of atoms in the molecular system

maxtyp maximum number of force field atom type definitions
maxclass maximum number of force field atom class definitions
maxval maximum number of atoms directly bonded to an atom
maxref maximum number of stored reference molecular systems
maxgrp maximum number of user-defined groups of atoms
maxres maximum number of residues in the macromolecule
maxfix maximum number of geometric constraints and restraints
maxbio maximum number of biopolymer atom definitions

SOCKET Module socket communication control parameters

skttyp socket information type (1=DYN, 2=OPT)

cstep current dynamics or optimization step number
cdt current dynamics cumulative simulation time
cenergy current potential energy from simulation
sktstart logical flag to indicate socket initialization
sktstop logical flag to indicate socket shutdown
use_socket logical flag governing use of external sockets

SOLPOT Module solvation term functional form details

solvtyp type of continuum solvation energy model in use

borntyp method to be used for the Born radius computation

SOLUTE Module continuum solvation model parameters

doffset dielectric offset to continuum solvation atomic radii

onipr probe radius to use with onion Born radius method
p1 single-atom scale factor for analytical Still radii
p2 1-2 interaction scale factor for analytical Still radii
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p3 1-3 interaction scale factor for analytical Still radii
p4 nonbonded scale factor for analytical Still radii
p5 soft cutoff parameter for analytical Still radii
descoff offset for pairwise descreening at small separation
rneck atom radius bins used to store Aij/Bij neck constants
aneck constants to use in calculating neck values
bneck constants to use in calculating neck values
rsolv atomic radius of each atom for continuum solvation
rdescr atomic radius of each atom for descreening
asolv atomic surface area solvation parameters
rborn Born radius of each atom for GB/SA solvation
drb solvation derivatives with respect to Born radii
drbp GK polarization derivatives with respect to Born radii
drobc chain rule term for Onufriev-Bashford-Case radii
gpol polarization self-energy values for each atom
shct overlap scale factors for Hawkins-Cramer-Truhlar radii
aobc alpha values for Onufriev-Bashford-Case radii
bobc beta values for Onufriev-Bashford-Case radii
gobc gamma values for Onufriev-Bashford-Case radii
vsolv atomic volume of each atom for use with ACE
wace "omega" values for atom class pairs for use with ACE
s2ace "sigma^2" values for atom class pairs for use with ACE
uace "mu" values for atom class pairs for use with ACE
sneck pairwise neck correction scale factor for each atom
bornint unscaled 1/r^6 corrections for tanh chain rule term
useneck logical flag to use neck interstitial space correction
usetanh logical flag to use tanh interstitial space correction

STODYN Module SD trajectory frictional coefficients

friction global frictional coefficient for exposed particle

fgamma atomic frictional coefficients for each atom
use_sdarea logical flag to use surface area friction scaling

STRBND Module stretch-bends in current structure

nstrbnd total number of stretch-bend interactions

isb angle and bond numbers used in stretch-bend
sbk force constants for stretch-bend terms

STRTOR Module stretch-torsions in current structure

nstrtor total number of stretch-torsion interactions

ist torsion and bond numbers used in stretch-torsion
kst 1-, 2- and 3-fold stretch-torsion force constants

SYNTRN Module synchronous transit path definition

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tpath value of the path coordinate (0=reactant, 1=product)

ppath path coordinate for extra point in quadratic transit
xmin1 reactant coordinates as array of optimization variables
xmin2 product coordinates as array of optimization variables
xm extra coordinate set for quadratic synchronous transit

TARRAY Module store dipole-dipole matrix elements

ntpair number of stored dipole-dipole matrix elements

tindex index into stored dipole-dipole matrix values
tdipdip stored dipole-dipole matrix element values

TETTOR Module tetratorsions in the current structure

ntettor total number of tetratorsions in the system

itettor numbers of the atoms in each tetratorsion

TORPOT Module torsional functional form details

idihunit convert improper dihedral energy to kcal/mole

itorunit convert improper torsion amplitudes to kcal/mole
torsunit convert torsional parameter amplitudes to kcal/mole
ptorunit convert pi-system torsion energy to kcal/mole
storunit convert stretch-torsion energy to kcal/mole
atorunit convert angle-torsion energy to kcal/mole
ttorunit convert torsion-torsion energy to kcal/mole

TORS Module torsional angles in current structure

ntors total number of torsional angles in the system

itors numbers of the atoms in each torsional angle
tors1 1-fold amplitude and phase for each torsional angle
tors2 2-fold amplitude and phase for each torsional angle
tors3 3-fold amplitude and phase for each torsional angle
tors4 4-fold amplitude and phase for each torsional angle
tors5 5-fold amplitude and phase for each torsional angle
tors6 6-fold amplitude and phase for each torsional angle

TORTOR Module torsion-torsions in current structure

ntortor total number of torsion-torsion interactions

itt atoms and parameter indices for torsion-torsion

TREE Module potential smoothing search tree levels

maxpss maximum number of potential smoothing levels

nlevel number of levels of potential smoothing used
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etree energy reference value at the top of the tree
ilevel smoothing deformation value at each tree level

TRITOR Module tritorsions in the current structure

ntritor total number of tritorsions in the system

itritor numbers of the atoms in each tritorsion

UNITS Module physical constants and unit conversions

avogadro Avogadro's number (N) in particles/mole

lightspd speed of light in vacuum (c) in cm/ps
boltzmann Boltzmann constant (kB) in g*Ang**2/ps**2/mole/K
gasconst ideal gas constant (R) in kcal/mole/K
elemchg elementary charge of a proton in Coulombs
vacperm vacuum permittivity (electric constant, eps0) in F/m
emass mass of an electron in atomic mass units
planck Planck's constant (h) in J-s
joule conversion from calorie to joule
ekcal conversion from kcal to g*Ang**2/ps**2
bohr conversion from Bohr to Angstrom
hartree conversion from Hartree to kcal/mole
evolt conversion from Hartree to electron-volt
efreq conversion from Hartree to cm-1
coulomb conversion from electron**2/Ang to kcal/mole
elefield conversion from electron**2/Ang to megavolt/cm
debye conversion from electron-Ang to Debye
prescon conversion from kcal/mole/Ang**3 to Atm

UPRIOR Module previous values of induced dipoles

maxpred maximum number of predictor induced dipoles to save

nualt number of sets of prior induced dipoles in storage
maxualt number of sets of induced dipoles needed for predictor
gear coefficients for Gear predictor binomial method
aspc coefficients for always stable predictor-corrector
bpred coefficients for induced dipole predictor polynomial
bpredp coefficients for predictor polynomial in energy field
bpreds coefficients for predictor for PB/GK solvation
bpredps coefficients for predictor in PB/GK energy field
udalt prior values for induced dipoles at each site
upalt prior values for induced dipoles in energy field
usalt prior values for induced dipoles for PB/GK solvation
upsalt prior values for induced dipoles in PB/GK energy field
use_pred flag to control use of induced dipole prediction
polpred type of predictor polynomial (GEAR, ASPC or LSQR)

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UREY Module Urey-Bradley interactions in structure

nurey total number of Urey-Bradley terms in the system

iury numbers of the atoms in each Urey-Bradley interaction
uk Urey-Bradley force constants (kcal/mole/Ang**2)
ul ideal 1-3 distance values in Angstroms

URYPOT Module Urey-Bradley functional form details

cury cubic coefficient in Urey-Bradley potential

qury quartic coefficient in Urey-Bradley potential
ureyunit convert Urey-Bradley energy to kcal/mole

USAGE Module atoms active during energy computation

nuse total number of active atoms in energy calculation

iuse numbers of the atoms active in energy calculation
use true if an atom is active, false if inactive

VALFIT Module valence term parameter fitting values

fit_bond logical flag to fit bond stretch parameters

fit_angle logical flag to fit angle bend parameters
fit_strbnd logical flag to fit stretch-bend parameters
fit_urey logical flag to fit Urey-Bradley parameters
fit_opbend logical flag to fit out-of-plane bend parameters
fit_tors logical flag to fit torsional parameters
fit_struct logical flag to structure-fit valence parameters
fit_force logical flag to force-fit valence parameters

VDW Module van der Waals terms in current structure

nvdw total number van der Waals sites in the system

ivdw number of the atom for each van der Waals site
jvdw index into the vdw parameter matrix for each atom
mvdw index into the vdw parameter matrix for each class
ired attached atom from which reduction factor is applied
kred value of reduction factor parameter for each atom
xred reduced x-coordinate for each atom in the system
yred reduced y-coordinate for each atom in the system
zred reduced z-coordinate for each atom in the system
radmin minimum energy distance for each atom class pair
epsilon well depth parameter for each atom class pair
radmin4 minimum energy distance for 1-4 interaction pairs
epsilon4 well depth parameter for 1-4 interaction pairs
radhbnd minimum energy distance for hydrogen bonding pairs
epshbnd well depth parameter for hydrogen bonding pairs

VDWPOT Module van der Waals functional form details

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igauss coefficients of Gaussian fit to vdw potential

ngauss number of Gaussians used in fit to vdw potential
abuck value of "A" constant in Buckingham vdw potential
bbuck value of "B" constant in Buckingham vdw potential
cbuck value of "C" constant in Buckingham vdw potential
ghal value of "gamma" in buffered 14-7 vdw potential
dhal value of "delta" in buffered 14-7 vdw potential
v2scale factor by which 1-2 vdw interactions are scaled
v3scale factor by which 1-3 vdw interactions are scaled
v4scale factor by which 1-4 vdw interactions are scaled
v5scale factor by which 1-5 vdw interactions are scaled
use_vcorr flag to use long range van der Waals correction
vdwindex indexing mode (atom type or class) for vdw parameters
vdwtyp type of van der Waals potential energy function
radtyp type of parameter (sigma or R-min) for atomic size
radsiz atomic size provided as radius or diameter
radrule combining rule for atomic size parameters
epsrule combining rule for vdw well depth parameters
gausstyp type of Gaussian fit to van der Waals potential

VIBS Module iterative vibrational analysis components

rho trial vectors for iterative vibrational analysis

rhok alternate vectors for iterative vibrational analysis
rwork temporary work array for eigenvector transformation

VIRIAL Module components of internal virial tensor

vir total internal virial Cartesian tensor components

use_virial logical flag governing use of virial computation

WARP Module potential surface smoothing parameters

deform value of the smoothing deformation parameter

difft diffusion coefficient for torsional potential
diffv diffusion coefficient for van der Waals potential
diffc diffusion coefficient for charge-charge potential
m2 second moment of the GDA gaussian for each atom
use_smooth flag to use a potential energy smoothing method
use_dem flag to use diffusion equation method potential
use_gda flag to use gaussian density annealing potential
use_tophat flag to use analytical tophat smoothed potential
use_stophat flag to use shifted tophat smoothed potential

XTALS Module structures used for parameter fitting

maxlsq maximum number of least squares variables

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maxrsd maximum number of residual functions
nxtal number of molecular structures to be stored
nvary number of potential parameters to optimize
ivary index for the types of potential parameters
iresid structure to which each residual function refers
vary atom numbers involved in potential parameters
e0_lattice ideal lattice energy for the current crystal
varxtl type of each potential parameter to be optimized
rsdxtl experimental variable for each of the residuals

ZCLOSE Module Z-matrix ring openings and closures

nadd number of added bonds between Z-matrix atoms

ndel number of bonds between Z-matrix bonds to delete
iadd numbers of the atom pairs defining added bonds
idel numbers of the atom pairs defining deleted bonds

ZCOORD Module Z-matrix internal coordinate values

iz defining atom numbers for each Z-matrix atom

zbond bond length used to define each Z-matrix atom
zang bond angle used to define each Z-matrix atom
ztors angle or torsion used to define Z-matrix atom

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 CHAPTER

ELEVEN

TEST CASES & EXAMPLES

This section contains brief descriptions of the sample calculations found in the TEST subdirectory
of the Tinker distribution. These test cases exercise several of the current Tinker programs and are
intended to provide an overview of the capabilities of the package. In addition, a number of input
files for various molecular systems are provided in the EXAMPLE subdirectory.
ANION Test
Estimates the hydration free energy difference for Cl- vs. Br- anion via a 10 picosecond simulation
of a “hybrid” anion in a box of water, followed by free energy perturbation
ARGON Test
Performs an initial energy minimization on a periodic box containing 150 argon atoms, then per-
forms 25 picoseconds of molecular dynamics simulation, on a box with 150 argon atoms
CATION Test
Computes the hydration free energy difference for Rb+ vs. Cs+ cation via a 2 picosecond simula-
tion of each cation in a box of water, followed by a BAR free energy calculation
CLUSTER Test
Performs a set of 10 Gaussian density annealing (GDA) trials on a cluster of 13 argon atoms to find
the global minimum energy structure
CRAMBIN Test
Generates a Tinker XYZ file from a PDB file, followed by single point energy computation and
determination of the molecular volume and surface area
CYCLOHEXANE Test
Locates the transition state between chair and boat cyclohexane via two methods: the Muller-
Brown saddle point method, and path sampling using the Elber algorithm; vibrational analysis of
the results shows the same TS with one negative frequency
DHFR Test
Runs 10 steps of molecular dynamics on an equilibrated system of DHFR protein in water using the
AMOEBA force field; note this is the so-called Joint Amber-CHARMM “JAC” benchmark containing
23558 total atoms
DIALANINE Test

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Finds all the local minima of alanine dipeptide via a potential energy surface scan using torsional
modes to jump between minima
ENKEPHALIN Test
Builds coordinates for Met-enkephalin from amino acid sequence and phi/psi angles, followed by
truncated Newton energy minimization and determination of the lowest frequency normal mode
ETHANOL Test
Fits torsional parameter values for the ethanol C-C-O-H bond based on relative quantum mechani-
cal energies from Gaussian for rotating the C-O bond
FORMAMIDE Test
Generates a unit cell from fractional coordinates, followed by full crystal energy minimization and
determination of optimal carbonyl oxygen parameters via a fit to lattice energy and structure
GPCR Test
Finds the lowest-frequency bacteriorhodopsin normal mode using a sliding block iterative diago-
nalization; alter the gpcr.run script to save the file gpcr.001 if you want view of the mode; this
example can require up to an hour to complete
HELIX Test
Performs rigid-body optimization of the packing of two ideal polyalanine helices using only van der
Waals interactions
ICE Test
Performs a short MD simulation of the monoclinic ice V crystal form using the iAMOEBA water
model, pairwise neighbor lists and PME electrostatics
IFABP Test
Generates three distance geometry structures for intestinal fatty acid binding protein from a set of
NOE distance restraints and torsional restraints.
LIQUID Test
Prints the system setup and computes the force field energy components for three small liquid water
boxes using the AMOEBA, AMOEBA+ and HIPPO force fields
METHANOL Test
Processes distributed multipole analysis (DMA) output to extract coordinates and permanent multi-
poles, set local frames and polarization groups, modify the intramolecular polarization, detect and
average equivalent atomic sites
NITROGEN Test
Calculates the self-diffusion constant and the N-N radial distribution function for liquid nitrogen
via analysis of a 50 picosecond MD trajectory
POLYALA Test
Generates an extended conformation of capped alanine octapeptide, then uses Monte Carlo Mini-
mization with torsion moves to find the 3/10 helix global minimum

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PYRIDINE Test
Converts a simple XYZ file for pyridine to Tinker XYZ format using the BASIC force field, and
computes the molecular mechanics energy
SALT Test
Converts a sodium chloride assymetric unit to the corresponding unit cell, then minimizes the crys-
tal starting from the diffraction structure using Ewald summation to model long-range electrostatics
VASOPRESSIN Test
Compares analytical and finite difference numerical gradients over Cartesian and internal coordi-
nates for vasopressin using the AMOEBA force field model
WATER Test
Fits the electrostatic potential for the TIP3P, AMOEBA and HIPPO water models to a QM-derived
potential at the MP2/aug-cc-pVTZ level on a grid of points outside the molecular surface

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 CHAPTER

TWELVE

BENCHMARK RESULTS

The tables in this section provide CPU benchmarks for basic Tinker energy and derivative evalua-
tions, vibrational analysis and molecular dynamics simulation. All times are in seconds and were
measured with Tinker executables dimensioned to a maximum of 1000000 atoms. Each bench-
mark was run on an unloaded machine and is the fastest time reported for that particular machine.
The first five benchmarks are run serial on a single thread, while the last four benchmarks reflect
OpenMP parallel performance.

12.1 Calmodulin Energy Evaluation (Serial)

Gas-Phase Calmodulin Molecule, 2264 Atoms, Amber ff94 Force Field, No Nonbonded Cutoffs, 100
Evaluations
Machine Type (OS/Compiler) CPU Energy Gradient Hessian

Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 5.6 10.6 37.1
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 3.1 6.1 20.4
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 5.7 9.8 36.3

12.2 Crambin Crystal Energy Evaluation (Serial)

Crambin Unit Cell, 1360 Atoms in Periodic Unit Cell, OPLS-UA Force Field with PME Electrostatics,
9.0 Ang vdw Cutoff, 1000 Evaluations
Machine Type (OS/Compiler) CPU Energy Gradient Hessian

Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 14.6 18.6 67.8
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 10.5 13.0 49.7
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 13.6 17.5 70.6

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12.3 Crambin Normal Mode Calculation (Serial)

Hessian Eigenvalues, Normal Modes and Vibrational Freqencies for the 42-Amino Acid, 642-Atom
Protein Crambin, CHARMM-22 Force Field with Cutoffs
Machine Type (OS/Compiler) CPU Seconds

Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 10.8
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 15.3
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 11.0

12.4 Water Box Molecular Dynamics using TIP3P (Serial)

MD run of 10000 Steps for 216 TIP3P Waters in 18.643 Ang Periodic Box, 9.0 Ang Shifted &
Switched Cutoffs, Rattle for Rigid TIP3P, 1.0 fs Time Step with Modified Beeman Integrator
Machine Type (OS/Compiler) CPU Seconds

Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 55.6
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 49.1
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 54.4

12.5 Water Box Molecular Dynamics using AMOEBA (Serial)

MD run of 1000 Steps for 216 AMOEBA Waters in a 18.643 Ang Box, Neighbor Lists, PME with a
20x20x20 FFT and 7.0 Ang Real-Space Cutoff, 9.0 Ang vdW Cutoff with Correction, 1.0 fs Time
Step with Modified Beeman Integrator, and 0.00001 RMS Induced Dipole Convergence
Machine Type (OS/Compiler) CPU Seconds

Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 37.5
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 26.2
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 38.0

12.6 MD on DHFR in Water using CHARMM (OpenMP Parallel)

MD run of 100 Steps for CHARMM DHFR in Water (23558 Atoms, 62.23 Ang Box), Neighbor Lists,
PME with a 64x64x64 FFT and 7.0 Ang Real-Space Cutoff, 9.0 Ang vdW Cutoff, 1.0 fs Time Step
with Modified Beeman Integrator; OpenMP timings as “wall clock” time, with parallel speedup in
parentheses
Machine Type (OS/Compiler) CPU Core/Thread Seconds

252 Chapter 12. Benchmark Results

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Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/1 32.9 (1.00)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/2 23.0 (1.43)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/4 15.6 (2.11)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/6 12.8 (2.57)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/12 11.1 (2.96)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/1 26.8 (1.00)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/2 18.1 (1.48)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/4 12.4 (2.16)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/8 9.4 (2.85)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/1 32.5 (1.00)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/2 22.1 (1.47)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/4 15.4 (2.11)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/6 13.0 (2.50)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/12 12.8 (2.54)

12.7 MD on DHFR in Water using AMOEBA (OpenMP Parallel)

MD run of 100 Steps for AMOEBA DHFR in Water (23558 Atoms, 62.23 Ang Box), Neighbor Lists,
PME with a 64x64x64 FFT and 7.0 Ang Real-Space Cutoff, 9.0 Ang vdW Cutoff with Correction,
1.0 fs Time Step with Modified Beeman Integrator, and 0.00001 RMS Induced Dipole Convergence;
OpenMP timings reported as “wall clock” time, with parallel speedup in parentheses
Machine Type (OS/Compiler) CPU Core/Thread Seconds

Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/1 157.0 (1.00)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/2 100.1 (1.57)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/4 63.0 (2.49)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/6 52.0 (3.02)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/12 47.6 (3.30)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/1 102.5 (1.00)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/2 64.4 (1.59)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/4 40.9 (2.51)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/8 31.4 (3.26)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/1 154.8 (1.00)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/2 99.9 (1.55)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/4 66.2 (2.34)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/6 55.1 (2.81)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/12 60.7 (2.55)

12.7. MD on DHFR in Water using AMOEBA (OpenMP Parallel) 253

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12.8 MD on COX-2 in Water using OPLS-AA (OpenMP Parallel)

MD run of 100 Steps for OPLS-AA COX-2 in Water (174219 Atoms, 120.0 Ang Box), Neighbor Lists,
PME with a 128x128x128 FFT and 7.0 Ang Real-Space Cutoff, 9.0 Ang vdW Cutoff, 1.0 fs Time
Step with Modified Beeman Integrator; RATTLE for all X-H bonds and rigid TIP3P Water; OpenMP
timings reported as “wall clock” time, with parallel speedup in parentheses
Machine Type (OS/Compiler) CPU Core/Thread Seconds

Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/1 236.1 (1.00)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/2 178.8 (1.32)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/4 122.9 (1.92)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/6 106.3 (2.22)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/12 99.2 (2.38)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/1 180.6 (1.00)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/2 133.3 (1.35)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/4 91.8 (1.97)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/8 77.4 (2.33)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/1 243.1 (1.00)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/2 183.6 (1.32)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/4 128.1 (1.90)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/6 110.5 (2.20)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/12 105.9 (2.30)

12.9 MD on COX-2 in Water using AMOEBA (OpenMP Parallel)

MD run of 100 Steps for AMOEBA COX-2 in Water (174219 Atoms, 120.0 Ang Box), Neighbor Lists,
PME with a 128x128x128 FFT and 7.0 Ang Real-Space Cutoff, 9.0 Ang vdW Cutoff with Correction,
1.0 fs Time Step with Modified Beeman Integrator, and 0.00001 RMS Induced Dipole Convergence;
OpenMP timings reported as “wall clock” time, with parallel speedup in parentheses
Machine Type (OS/Compiler) CPU Core/Thread Seconds

Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/1 1625.8 (1.00)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/2 1112.8 (1.46)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/4 658.7 (2.47)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/6 530.5 (3.06)
Mac Mini 2018 (macOS 15.4, GNU 14.2) Intel Core i7 6/12 484.2 (3.36)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/1 1086.2 (1.00)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/2 721.7 (1.51)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/4 437.3 (2.48)
MacBook Air 15 (macOS 15.1, GNU 14.1) Apple M2 8/8 344.5 (3.15)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/1 1691.0 (1.00)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/2 1148.6 (1.47)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/4 702.8 (2.41)
(continues on next page)

254 Chapter 12. Benchmark Results

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(continued from previous page)

Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/6 577.5 (2.93)
Razer Blade 15 (Ubuntu 24.04, GNU 13.3) Intel 9750H 6/12 557.8 (3.03)

12.9. MD on COX-2 in Water using AMOEBA (OpenMP Parallel) 255

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256 Chapter 12. Benchmark Results

 CHAPTER

THIRTEEN

ACKNOWLEDGMENTS

The Tinker package has developed over a period of many years, very slowly during the late-1980s,
and more rapidly since the mid-1990s in Jay Ponder’s research group at the Washington University
School of Medicine and the Department of Chemistry at Washington Univeristy in Saint Louis.
Many people have played significant roles in the development of the package into its current form.
The major contributors are listed below:
Stew Rubenstein
coordinate interconversions; original optimization methods and torsional angle manipulation
Craig Kundrot
molecular surface area & volume and their derivatives
Shawn Huston
original Amber/OPLS implementation; free energy calculations; time correlation functions
Mike Dudek
initial multipole models for peptides and proteins
Yong “Mike” Kong
multipole electrostatics; dipole polarization; reaction field treatment; Tinker water model
Reece Hart
potential smoothing methodology; Scheraga’s DEM, Straub’s GDA and extensions
Mike Hodsdon
extension of the Tinker distance geometry program and its application to NMR NOE structure
determination
Rohit Pappu
potential smoothing methodology and PSS algorithms; rigid body optimization; GB/SA solvation
derivatives
Wijnand Mooij
MM3 directional hydrogen bonding term; crystal lattice minimization code
Gerald Loeffler

257
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stochastic/Langevin dynamics implementation

Marina Vorobieva & Nina Sokolova
nucleic acid building module and parameter translation
Peter Bagossi
AMOEBA force field parameters for alkanes and diatomics
Pengyu Ren
Ewald summation for polarizable atomic multipoles; AMOEBA force field for water, organics and
peptides
Anders Carlsson
original ligand field potential energy term for transition metals
Andrey Kutepov
integrator for rigid-body dynamics trajectories
Tom Darden
Particle Mesh Ewald (PME) code, and development of PME for the AMOEBA force field
Alan Grossfield
Monte Carlo minimization; tophat potential smoothing
Michael Schnieders
Force Field Explorer GUI for Tinker; neighbor lists for nonbonded interactions
Chuanjie Wu
solvation free energy calculations; AMOEBA nucleic acid force field; parameterization tools for
Tinker
Justin Xiang
angular overlap and valence bond potential models for transition metals
David Gohara
OpenMP parallelization of energy terms including PME, and parallel neighbor lists
Chao Lu
derivatives of potential energy with respect to lambda for metadynamics and similar methods
Aaron Gordon
enthalpy and entropy estimates as an adjunct to BAR free energy calculation
Zhi Wang
Bennett acceptance ratio (BAR) for free energy calculations; lead developer for Tinker9 GPU code
Josh Rackers

258 Chapter 13. Acknowledgments

 Tinker User's Guide

derivation and implementation of potentials for the HIPPO force field, and elaboration of the HIPPO
water model
Rose Silva
force field parameterization tools and the HIPPO force field for general organic molecules
Rae Corrigan
improved algorithms and parameterization for the Generalized Kirkwood implicit solvation model
the polarizable multipole electrostatics
Moses Chung
parameterization and development of HIPPO model for ions; AlphaMol surface area and volume
calculations
It is critically important that Tinker’s distributed force field parameter sets exactly reproduce the
intent of the original force field authors. We would like to thank Julian Tirado-Rives (OPLS-AA),
Alex MacKerell (CHARMM27), Wilfred van Gunsteren (GROMOS), and Adrian Roitberg and Carlos
Simmerling (Amber) for their help in testing Tinker’s results against those given by the authentic
programs and parameter sets. Lou Allinger provided updated parameters for MM2 and MM3 on
several occasions. His very successful methods provided the original inspiration for the develop-
ment of Tinker.
Still other workers have devoted considerable time in developing code that will hopefully be in-
corporated into future Tinker versions; for example, Jim Kress (UFF implementation) and Michael
Sheets (numerous code optimizations, thermodynamic integration). Finally, we wish to thank the
many users of the Tinker package for their suggestions and comments, praise and criticism, which
have resulted in a variety of improvements.

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260 Chapter 13. Acknowledgments

 CHAPTER

FOURTEEN

REFERENCES

This section contains a list of the references to general theory, algorithms and implementation
details which have been of use during the development of the Tinker package. Methods described
in some of the references have been implemented in detail within the Tinker source code. Other
references contain useful background information although the algorithms themselves are now
obsolete. Still other papers contain ideas or extensions planned for future inclusion in Tinker.
References for specific force field parameter sets are provided in an earlier section of this User’s
Guide. This list is heavily skewed toward biomolecules in general and proteins in particular. This
bias reflects our group’s major interests; however an attempt has been made to include methods
which should be generally applicable.

14.1 Molecular Mechanics & Dynamics Software Packages

14.1.1 Tinker Software Tools

Tinker
Tinker 8: Software Tools for Molecular Design, J. A. Rackers, Z. Wang, C. Lu, M. L. Laury, L.
Lagardere, M. J. Schnieders, J.-P. Piquemal, P. Ren and J. W. Ponder, J. Chem. Theory Comput.,
14, 5273-5289 (2018)
Tinker-HP
Tinker-HP: A Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large
Complex Systems with Advanced Point Dipole Polarizable Force Fields, L. Lagardere, L.-H. Jolly, F.
Lipparini, F. Aviat, B. Stamm, Z. F. Jing, M. Harger, H. Torabifard, G. A. Cisneros, M. J. Schnieders,
N. Gresh, Y. Maday, P. Y. Ren, J. W. Ponder and J.-P. Piquemal, Chem. Sci., 9, 956-972 (2018)
Tinker-OpenMM
Tinker-OpenMM: Absolute and Relative Alchemical Free Energies Using AMOEBA on GPUs, M.
Harger, D. Li, Z. Wang, K. Dalby, L. Lagardere, J.-P. Piquemal, J. Ponder and P. Ren, J. Comput.
Chem., 38, 2047-2055 (2017)

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14.1.2 Alternative Molecular Modeling Software

AMBER Peter Kollman, University of California, San Francisco

AMMP Robert Harrison, Georgia State University, Atlanta
ARGOS J. Andrew McCammon, University of California, San Diego
BOSS William Jorgensen, Yale University
BRUGEL Shoshona Wodak, Free University of Brussels
CFF Shneior Lifson, Weizmann Institute
CHARMM Martin Karplus, Harvard University
DELPHI Bastian van de Graaf, Delft University of Technology
DISCOVER Molecular Simulations Inc., San Diego
DL_POLY Ilian Todorov & W. Smith, STFC Daresbury Laboratory
ECEPP Harold Scheraga, Cornell University
ENCAD Michael Levitt, Stanford University
FANTOM Werner Braun, University of Texas, Galveston
FEDER/2 Nobuhiro Go, Kyoto University
GROMACS Erik Lindahl, Stockholm University
GROMOS Wilfred van Gunsteren, BIOMOS and ETH, Zurich
IMPACT Ronald Levy, Temple University, Philadelphia
MACROMODEL Schodinger, Inc., New York
MM2/MM3/MM4 N. Lou Allinger, University of Georgia
MMC Cliff Dykstra, Indiana Univ.-Purdue Univ. at Indianapolis
MMFF Thomas Halgren, Merck Research Laboratories, Rahway, NJ
MMTK Konrad Hinsen, Inst. of Structural Biology, Grenoble
MOIL Ron Elber, Cornell University
MOLARIS Arieh Warshel, University of Southern California
MOLDY Keith Refson, Oxford University
MOSCITO Dietmar Paschek & Alfons Geiger, Universitat Dortmund
NAMD Klaus Schulten, University of Illinois, Urbana
OOMPAA J. Andrew McCammon, University of California, San Diego
OPENMM Peter Eastman & Vijay Pande, Stanford University
ORAL Karel Zimmerman, INRA, Jouy-en-Josas, France
ORIENT Anthony Stone, Cambridge University
PCMODEL Kevin Gilbert, Serena Software, Bloomington, Indiana
PEFF Jan Dillen, University of Pretoria, South Africa
PHENIX Paul Adams, Lawrence Berkeley Laboratory
Q Johan Aqvist, Uppsala University
SIBFA Nohad Gresh, INSERM, CNRS, Paris
SIGMA Jan Hermans, University of North Carolina
SPASIBA Gerard Vergoten, Universite de Lille
SPASMS David Spellmeyer and the Kollman Group, UCSF
UTAH5 Cornelis Altona, Leiden University, Netherlands
XPLOR/CNS Axel Brunger, Stanford University
YAMMP Stephen Harvey, University of Alabama, Birmingham
YASP Florian Mueller-Plathe, TU Darmstadt
YETI Angelo Vedani, Biografik-Labor 3R, Basel

262 Chapter 14. References

 Tinker User's Guide

AMBER
An Overview of the Amber Biomolecular Simulation Package, R. Salomon-Ferrer, D. A. Case, R. C.
Walker, WIREs Comput. Mol. Sci. 3, 198-210 (2013)
The Amber Biomolecular Simulation Programs. D. A. Case, T. E. Cheatham, III, T. Darden, H.
Gohlke, R. Luo, K. M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. J. Comput.
Chem., 26, 1668-1688 (2005)
AMBER, a Package of Computer Programs for Applying Molecular Mechanics, Normal Mode Anal-
ysis, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic
Properties of Molecules, D. A Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham III,
S. DeBolt, D. Ferguson, G. Seibel and P. Kollman, Comp. Phys. Commun., 91, 1-41 (1995)
AMMP
Stiffness and Energy Conservation in Molecular Dynamics: An Improved Integrator, R. W. Harrison,
J. Comput. Chem., 14, 1112-1122 (1993)
ARGOS
ARGOS, a Vectorized General Molecular Dynamics Program, T. P. Straatsma and J. A. McCammon,
J. Comput. Chem., 11, 943-951 (1990)
BOSS
Molecular Modeling of Organic and Biomolecular Systems Using BOSS and MCPRO, W. L. Jor-
gensen and J. Tirado-Rives, J. Comput. Chem., 26, 1689-1700 (2005)
BRUGEL
Interactive Computer Animation of Macromolecules, P. Delhaise, M. Bardiaux and S. Wodak, J.
Mol. Graphics, 2, 103-106 (1984)
CHARMM
CHARMM: The Biomolecular Simulation Program, B. R. Brooks, C. L. Brooks III, A. D. Mackerell, L.
Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch A. Caflisch, L. Caves, Q.
Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma,
V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L.
Woodcock, X. Wu, W. Yang, D. M. York, and M. Karplus, J. Comput. Chem., 30, 1545-1615 (2009)
CHARMM: The Energy Function and Its Parameterization with an Overview of the Program, A. D.
MacKerell, Jr., B. Brooks, C. L. Brooks, III, L. Nilsson, B. Roux, Y. Won, and M. Karplus, in The
Encyclopedia of Computational Chemistry, Vol. 1, pg. 271-277, John Wiley & Sons, Chichester,
1998
CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, B. R.
Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus, J. Comput.
Chem., 4, 187-217 (1983)
DELPHI
Delft Molecular Mechanics: A New Approach to Hydrocarbon Force Fields. Inclusion of a Geometry-
Dependent Charge Calculation, A. C. T. van Duin, J. M. A. Baas and B. van de Graaf, J. Chem. Soc.
Faraday Trans., 90, 2881-2895 (1994)

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Tinker User's Guide

DL_POLY
DL_POLY_3: New Dimensions in Molecular Simulations via Massive Parallelism, I. T. Todorov, W.
Smith, K. Trachenko and M. T. Dove, J. Mater. Chem., 16, 1911-1918 (2006)
ENCAD
Potential Energy Function and Parameters for Simulations for the Molecular Dynamics of Proteins
and Nucleic Acids in Solution, M. Levitt, M. Hirshberg, R. Sharon and V. Daggett, Comp. Phys.
Commun., 91, 215-231 (1995)
FANTOM
The Program FANTOM for Energy Refinement of Polypeptides and Proteins Using a Newton-
Raphson Minimizer in Torsion Angle Space, T. Schaumann, W. Braun and K. Wurtrich, Biopolymers,
29, 679-694 (1990)
FEDER/2
FEDER/2: Program for Static and Dynamic Conformational Energy Analysis of Macro-molecules in
Dihedral Angle Space, H. Wako, S. Endo, K. Nagayama and N. Go, Comp. Phys. Commun., 91,
233-251 (1995)
GROMACS
GROMACS: High Performance Molecular Simulations Through Multi-Level Parallelism from Lap-
tops to Supercomputers, M. J. Abraham, T. Murtola, R. Schultz, S. Pall, J. C. Smith, B. Hess and E.
Lindahl, SoftwareX, 1-2, 19-25 (2015)
GROMACS 4.5: A High-Throughput and Highly Parallel Open Source Molecular Simulation Toolkit,
S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M.
Kasson, D. van der Spoel, B. Hess and E. Lindahl, Bioinformatics, 29, 845-854 (2013)
GROMACS 3.0: A Package for Molecular Simulation and Trajectory Analysis, E. Lindahl, B. Hess
and D. van der Spoel, J. Mol. Model., 7, 306-317 (2001)
GROMOS
The GROMOS Biomolecular Simulation Program Package, W. R. P. Scott, P. H. Hunenberger , I. G.
Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Kruger, W. F. van Gunsteren, J.
Phys. Chem. A, 103, 3596-3607 (1999)
IMPACT
Integrated Modeling Program, Applide Chemical Theory (IMPACT), J. L. Banks, H. S. Beard, Y. Cao,
A. E. Cho, W. Damm, R. Farid, A. K. Felts, T. A. Halgren, D. T. Mainz, J. R. Maple, R. Murphy, D.
M. Philipp, M. P. Repasky, L. Y. Zhang, B. J. Berne, R. A. Friesner, E. Gallicchio and R. M. Levy, J.
Comput. Chem., 26, 1752-1780 (2005)
MACROMODEL
MacroModel: An Integrated Software System for Modeling Organic and Bioorganic Molecules Us-
ing Molecular Mechanics, F. Mahamadi, N. G. J. Richards, W. C. Guida, R. Liskamp, M. Lipton, C.
Caufield, G. Chang, T. Hendrickson and W. C. Still, J. Comput. Chem., 11, 440-467 (1990)
MM2

264 Chapter 14. References

 Tinker User's Guide

Conformational Analysis. 130. MM2. A Hydrocarbon Force Field Utilizing V1 and V2 Torsional
Terms, N. L. Allinger, J. Am. Chem. Soc., 99, 8127-8134 (1977)
MM3
Molecular Mechanics. The MM3 Force Field for Hydrocarbons, N. L. Allinger, Y. H. Yuh and J.-H.
Lii, J. Am. Chem. Soc., 111, 8551-8566 (1989)
MM4
An Improved Force Field (MM4) for Saturated Hydrocarbons, N. L. Allinger, K. Chen and J.-H. Lii,
J. Comput. Chem., 17, 642-668 (1996)
MMC
Molecular Mechanics for Weakly Interacting Assemblies of Rare Gas Atoms and Small Molecules,
C. E. Dykstra, J. Am. Chem. Soc., 111, 6168-6174 (1989)
MMFF
Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94,
T. A. Halgren, J. Comput. Chem., 17, 490-516 (1996)
MOIL
MOIL: A Program for Simulations of Macromolecules, R. Elber, A. Roitberg, C. Simmerling, R.
Goldstein, H. Li, G. Verkhiver, C. Keasar, J. Zhang and A. Ulitsky, Comp. Phys. Commun., 91,
159-189 (1995)
MOSCITO
Information available at the site http://139.30.122.11/MOSCITO/
NAMD
Scalable Molecular Dynamics with NAMD, J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhor-
shid, E. Villa, C. Chipot, R. D. Skeel, L. Kale and K. Schulten, J. Comput. Chem., 26, 1781-1802
(2005)
OOMPAA
OOMPAA: Object-oriented Model for Probing Assemblages of Atoms, G. A. Huber and J. A. McCam-
mon, J. Comput. Phys., 151, 264-282 (1999)
ORAL
ORAL: All Purpose Molecular Mechanics Simulator and Energy Minimizer, K. Zimmermann, J. Com-
put. Chem., 12, 310-319 (1991)
ORIENT
Orient: A Program for Studying Interactions Between Molecules, Version 5.0, A. J. Stone, A. Dull-
weber, O. Engkvist, E. Fraschini, M. P. Hodges, A. W. Meredith, D. R. Nutt, P. L. A. Popelier and D.
J. Wales, University of Cambridge, 2018
Information available at the site http://www-stone.ch.cam.ac.uk/programs.html#Orient/
PCMODEL

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PCMODEL V9.0: Molecular Modeling Software, User’s Manual, Serena Software, Bloomington, IN,
2004
PEFF
PEFF: A Program for the Development of Empirical Force Fields, J. L. M. Dillen, J. Comput. Chem.,
13, 257-267 (1992)
PHENIX
Macromolecular Structure Determination Using X-rays, Neutrons and Electrons: Recent Develop-
ments in Phenix, D. Liebschner, P. V. Afonine, M. L. Baker, G. Bunkóczi, V. B. Chen, T. I. Croll, B.
Hintze, L.-W. Hung, S. Jain, A. J. McCoy, N. W. Moriarty, R. D. Oeffner, B. K. Poon, M. G. Prisant,
R. J. Read, J. S. Richardson, D. C. Richardson, M. D. Sammito, O. V. Sobolev, D. H. Stockwell, T.
C. Terwilliger, A. G. Urzhumtsev, L. L. Videau, C. J. Williams and P. D. Adams, Acta Cryst., D75,
861-877 (2019)
Q
Q: A Molecular Dynamics Program for Free Energy Calculations and Empirical Valene Bond Simula-
tions in Biomolecular Systems, J. Marelius, K. Kolmodin, I. Feierberg and J. Aqvist, J. Mol. Graphics
Modell., 16, 213-225 (1998)
SIBFA
Inter- and Intramolecular Interactions. Inception and Refinements of the SIBFA, Molecular Me-
chanics (SMM) Procedure, a Separable, Polarizable Methodology Grounded on ab Initio SCF/MP2
Computations. Examples of Applications to Molecular Recognition Problems, N. Gresh, J. Chim.
Phys. PCB, 94, 1365-1416 (1997)
SIGMA
The Sigma MD Program and a Generic Interface Applicable to Multi-Functional Programs with
Complex, Hierarchical Command Structure, G. Mann, R. Yun, L. Nyland, J. Prins, J. Board and J.
Hermans, in Computational Methods for Macromolecules: Challenges and Applications, T. Schlick
and H.-H. Gan, Eds., Springer, 2002
UTAH5
UTAH5: A Versatile Programme Package for the Calculation of Molecular Properties by Force Field
Methods, D. H. Faber and C. Altona, Computers & Chemistry, 1, 203-213 (1977)
YAMMP
Yammp: Development of a Molecular Mechanics Program Using the Modular Programming
Method, R. K.-Z. Tan and S. C. Harvey, J. Comput. Chem., 14, 455-470 (1993)
YASP
YASP: A Molecular Simulation Package, F. Mueller-Plathe, Comput. Phys. Commun., 78, 77-94
(1993)
YETI
YETI: An Interactive Molecular Mechanics Program for Small-Molecule Protein Complexes, A.
Vedani, J. Comput. Chem., 9, 269-280 (1988)

266 Chapter 14. References

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14.2 Literature References by Topic

14.2.1 Molecular Mechanics Methodology

Molecular Mechanics, U. Burkert and N. L. Allinger, American Chemical Society, Washington, D.C.,
1982
Molecular Structure: Understanding Steric and Electronic Effects from Molecular Mechanics, N. L.
Allinger and D. W. Rogers, John Wiley & Sons, Hoboken, New Jersey, 2010
Molecular Modeling of Inorganic Compounds, 2nd Ed., P. Comba and T. W. Hambley, Wiley-VCH,
New York, 2001
Principles of Molecular Mechanics, K. Machida, Kodansha/John Wiley & Sons, Tokyo/New York,
1999
Molecular Mechanics Across Chemistry, A. K. Rappe and C. J. Casewit, University Science Books,
Sausalito, CA, 1997
Potential Energy Functions in Conformational Analysis (Lecture Notes in Chemistry, Vol. 27), K.
Rasmussen, Springer-Verlag, Berlin, 1985

14.2.2 Intermolecular Interactions

The Theory of Intermolecular Forces, 2nd Ed., A. J. Stone, Oxford University Press, 2013
Intermolecular and Surface Forces, 3rd Ed., J. N. Israelachvili, Academic Press, Amsterdam, 2013
Intermolecular Forces: Their Origin and Determination, G. C. Maitland, M. Rigby, E. B. Smith and
W. A. Wakeham, Oxford University Press, 1981

14.2.3 Computer Simulation Methodology

Computer Simulation of Liquids, M. P. Allen and D. J. Tildesley, Oxford University Press, Oxford,
1987
Essentials of Computational Chemistry: Theories and Models, C. J. Cramer, John Wiley and Sons,
New York, 2002
A Practical Introduction to the Simulation of Molecular Systems, M. J. Field, Cambridge Univ. Press,
Cambridge, 1999
Understanding Molecular Simulation: From Algorithms to Applications, 2nd Ed., D. Frankel and B.
Smit, Academic Press, San Diego, CA, 2001
Molecular Dynamics Simulation: Elementary Methods, J. M. Haile, John Wiley and Sons, New York,
1992
Introduction to Computational Chemistry, F. Jensen, John Wiley and Sons, New York, 1998
Molecular Modelling: Principles and Applications, 2nd Ed., A. R. Leach, Addison Wesley Longman,
Essex, England, 2001

14.2. Literature References by Topic 267

Tinker User's Guide

The Art of Molecular Dynamics Simulation, 2nd Ed., D. C. Rapaport, Cambridge University Press,
Cambridge, 2004
Molecular Modeling and Simulation: An Interdisciplinary Guide, 2nd Ed., T. Schlick, Springer-
Verlag, New York, 2010

14.2.4 Modeling of Biological Macromolecules

Computational Biochemistry and Biophysics, O. M. Becker, A. D. MacKerell, Jr., B. Roux and M.

Watanabe, Eds., Marcel Dekker, New York, 2001
Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics, C. L. Brooks III,
M. Karplus and B. M. Pettitt, John Wiley and Sons, New York, 1988
Protein Simulations (Advances in Protein Chemistry, Vol. 66), V. Daggett, Ed., Academic
Press/Elsevier, New York, 2003
Dynamics of Proteins and Nucleic Acids, J. A. McCammon and S. Harvey, Cambridge University
Press, Cambridge, 1987
Computer Simulation of Biomolecular Systems, Vol. 1-3, W. F. van Gunsteren, P. K. Weiner and A.
J. Wilkinson, Kluwer Academic Publishers, Dordrecht, 1989-1997

14.2.5 Nonlinear Optimization Algorithms

Numerical Optimization, 2nd Ed., J. Nocedal and S. J. Wright, Springer-Verlag, New York, 2006
Linear and Nonlinear Programming, 2nd Ed., I. Griva, S. G. Nash and A. Sofer, SIAM, Philadelphia,
2009
Practical Methods of Optimization, R. Fletcher, John Wiley & Sons Ltd., Chichester, 1987
Linear and Nonlinear Programming, 4th Ed., D. G. Luenberger and Y. Ye, Springer, New York, 2016
Practical Optimization, P. E. Gill, W. Murray and M. H. Wright, Academic Press, New York, 1981
Updating Quasi-Newton Matrices with Limited Storage, J. Nocedal, Math. Comp., 773-782 (1980)
A Stable, Rapidly Converging Conjugate Gradient Method for Energy Minimization, S. J. Watowich,
E. S. Meyer, R. Hagstrom and R. Josephs, J. Comput. Chem., 9, 650-661 (1988)
Optimally Conditioned Optimization Algorithms without Line Searches, W. C. Davidon, Math.
Prog., 9, 1-30 (1975)

268 Chapter 14. References

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14.2.6 Truncated Newton Optimization

An Efficient Newton-like Method for Molecular Mechanics Energy Minimization of Large Molecules,
J. W. Ponder and F. M. Richards, J. Comput. Chem., 8, 1016-1024 (1987)
Truncated-Newton Algorithms for Large-Scale Unconstrained Optimization, R. S. Dembo and T.
Steihaug, Math. Prog., 26, 190-212 (1983)
Choosing the Forcing Terms in an Inexact Newton Method, S. C. Eisenstat and H. F. Walker, SIAM
J. Sci. Comput., 17, 16-32 (1996)
A Powerful Truncated Newton Method for Potential Energy Minimization, T. Schlick and M. Over-
ton, J. Comput. Chem., 8, 1025-1039 (1987)
The Incomplete Cholesky-Conjugate Gradient Method for the Iterative Solution of Systems of Linear
Equations, D. S. Kershaw, J. Comput. Phys., 26, 43-65 (1978)
An Incomplete Factorization Technique for Positive Definite Linear Systems, T. A. Manteuffel, Math.
Comp., 34, 473-497 (1980)
A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications, P. Der-
reumaux, G. Zhang and T. Schlick and B. R. Brooks, J. Comput. Chem., 15, 532-552 (1994)
Direct Methods for Sparse Matrices, I. S. Duff, A. M. Erisman and J. K. Reid, Oxford University
Press, Oxford, 1986

14.2.7 Potential Energy Smoothing

Analysis and Application of Potential Energy Smoothing Methods for Global Optimization, R. V.
Pappu, R. K. Hart and J. W. Ponder, J. Phys. Chem. B, 102, 9725-9742 (1998)
The Multiple-Minima Problem in the Conformational Analysis of Molecules. Deformation of the
Potential Energy Hypersurface by the Diffusion Equation Method, L. Piela, J. Kostrowicki and H. A.
Scheraga, J. Phys. Chem., 93, 3339-3346 (1989)
Simulated Annealing Using the Classical Density Distribution, J. Ma and J. E. Straub, J. Chem.
Phys., 101, 533-541 (1994)
Cluster Structure Determination Using Gaussian Density Distribution Global Minimization Meth-
ods, C. Tsoo and C. L. Brooks, J. Chem. Phys., 101, 6405-6411 (1994)
Conformational Energy Minimization Using a Two-Stage Method, S. Nakamura, H. Hirose, M.
Ikeguchi and J. Doi, J. Phys. Chem., 99, 8374-8378 (1995)
Structure Optimization Combining Soft-Core Interaction Functions, the Diffusion Equation Method,
and Molecular Dynamics, T. Huber, A. E. Torda and W. F. van Gunsteren, J. Phys. Chem. A, 101,
5926-5930 (1997)
Finding Minimum-Energy Configurations of Lennard-Jones Clusters Using an Effective Potential, S.
Schelstraete and H. Verschelde, J. Phys. Chem. A, 101, 310-315 (1998)
Global Optimization Using Bad Derivatives: Derivative-Free Method for Molecular Energy Mini-
mization, I. Andricioaei and J. E. Straub, J. Comput. Chem., 19, 1445-1455 (1998)

14.2. Literature References by Topic 269

Tinker User's Guide

Search for the Most Stable Structures on Potential Energy Surfaces, L. Piela, Coll. Czech. Chem.
Commun., 63, 1368-1380 (1998)

14.2.8 “Sniffer” Global Optimization

Generalized Descent for Global Optimization, A. O. Griewank, J. Opt. Theor. Appl., 34, 11-39
(1981)
An Evaluation of the Sniffer Global Optimization Algorithm Using Standard Test Functions, R. A.
R. Butler and E. E. Slaminka, J. Comput. Phys., 99, 28-32 (1993)
Potential Transformation Methods for Large-Scale Global Optimization, J. W. Rogers and R. A.
Donnelly, SIAM J. Optim., 5, 871-891 (1995)

14.2.9 Integration Methods for Molecular Dynamics

Molecular Dynamics With Deterministic and Stochastic Numerical Methods, B. Leimkuhler and C.
Matthews, Springer, New York, 2015
Pushing the Limits of Multiple-Time-Step Strategies for Polarizable Point Dipole Molecular Dynam-
ics, L. Lagardere, F. Aviat and J.-P. Piquemal, J. Phys. Chem. Lett., 10, 2593-2599 (2019)
Some Multistep Methods for Use in Molecular Dynamics Calculations, D. Beeman, J. Comput. Phys.,
20, 130-139 (1976)
Integrating the Equations of Motion, M. Levitt and H. Meirovitch, J. Mol. Biol., 168, 617-620
(1983)
A Molecular Dynamics Study of the C-Terminal Fragment of the L7/L12 Ribosomal Protein, J.
Aqvist, W. F. van Gunsteren, M. Leijonmarck and O. Tapia, J. Mol. Biol., 183, 461-477 (1985)
A Computer Simulation Method for the Calculation of Equilibrium Constants for the Formation of
Physical Clusters of Molecules: Application to Small Water Clusters, W. C. Swope, H. C. Andersen,
P. H. Berens and K. R. Wilson, J. Chem. Phys., 76, 637-649 (1982)
A Multiple-Time-Step Molecular Dynamics Algorithm for Macromolecules, D. D. Humphreys, R. A.
Friesner and B. J. Berne, J. Phys. Chem., 98, 6885-6892 (1994)
Efficient Multiple-Time-Step Integrators with Distance-Based Force Splitting for Particle-Mesh-
Ewald Molecular Dynamics Simulations, X. Qian and T. Schlick, J. Chem. Phys., 115, 4019-4029
(2001)

270 Chapter 14. References

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14.2.10 Constraint Dynamics

Algorithms for Macromolecular Dynamics and Constraint Dynamics, W. F. van Gunsteren and H. J.
C. Berendsen, Mol. Phys., 34, 1311-1327 (1977)
Molecular Dynamics of Rigid Systems in Cartesian Coordinates: A General Formulation, G. Ciccotti,
M. Ferrario and J.-P. Ryckaert, Mol. Phys., 47, 1253-1264 (1982)
Rattle: A “Velocity” Version of the Shake Algorithm for Molecular Dynamics Calculations, H. C.
Andersen, J. Comput. Phys., 52, 24-34 (1983)
RATTLE Recipe for General Holonomic Constraints: Angle and Torsion Constraints, R. Kutteh, CCP5
Newsletter, 46, 9-17 (1998), available from the site https://www.ccp5.ac.uk/infoweb/newsletters/
Direct Application of SHAKE to the Velocity Verlet Algorithm, B. J. Palmer, J. Comput. Phys., 104,
470-472 (1993)
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithm for Rigid Water Models, S.
Miyamoto and P. A. Kollman, J. Comput. Chem., 13, 952-962 (1992)
LINCS: A Linear Constraint Solver for Molecular Simulations, B. Hess, H. Bekker, H. J. C. Berendsen
and J. G. E. M. Fraaije, J. Comput. Chem., 18, 1463-1472 (1997)
Non-Iterative Constraint Dynamics using Velocity-Explicit Verlet Methods, J. T. Slusher and P. T.
Cummings, Mol. Simul., 18, 213-224 (1996)

14.2.11 Langevin, Brownian and Stochastic Dynamics

Brownian Dynamics Simulation of a Chemical Reaction in Solution, M. P. Allen, Mol. Phys., 40,
1073-1087 (1980)
Algorithms for Brownian Dynamics, W. F. van Gunsteren and H. J. C. Berendsen, Mol. Phys., 45,
637-647 (1982)
A Rapidly Convergent Simulation Method: Mixed Monte Carlo/Stochastic Dynamics, F. Guarnieri
and W. C. Still, J. Comput. Chem., 15, 1302-1310 (1994)
Constant Temperature Simulations using the Langevin Equation with Velocity Verlet Integration,
M. G. Paterlini and D. M. Ferguson, Chem. Phys., 236, 243-252 (1998)

14.2.12 Constant Temperature and Pressure Dynamics

Molecular Dynamics with Coupling to an External Bath, H. J. C. Berendsen, J. P. M. Postma, W. F.

van Gunsteren, A. DiNola and J. R. Haak, J. Chem. Phys., 81, 3684-3690 (1984)
Canonical Dynamics: Equilibrium Phase-space Distributions, W. G. Hoover, Phys. Rev. A, 31, 1695-
1697 (1985)
Computer Simulation of a Phase Transition at Constant Temperature and Pressure, J. J. Morales, S.
Toxvaerd and L. F. Rull, Phys. Rev. A, 34, 1495-1498 (1986)
Algorithms for Molecular Dynamics at Constant Temperature and Pressure, B. R. Brooks, Internal
Report of Division of Computer Research and Technology, National Institutes of Health, 1988.

14.2. Literature References by Topic 271

Tinker User's Guide

Molecular Dynamics of Native Protein: Computer Simulation of Trajectories, M. Levitt, J. Mol.

Biol., 168, 595-620 (1983)

14.2.13 Out-of-Plane Deformation Terms

Derivation of Force Fields for Molecular Mechanics and Dynamics from ab initio Energy Surfaces,
J. R. Maple, U. Dinar and A. T. Hagler, Proc. Natl. Acad. Sci. USA, 85, 5350-5354 (1988)
New Out-of-Plane Angle and Bond Angle Internal Coordinates and Related Potential Energy Func-
tions for Molecular Mechanics and Dynamics Simulations, S.-H. Lee, K. Palmo and S. Krimm, J.
Comput. Chem., 20, 1067-1084 (1999)

14.2.14 Geometry-Dependent Charge Flux Terms

Geometry-Dependent Atomic Charges: Methodology and Application to Alkanes, Aldehydes, Ke-

tones, and Amides, U. Dinar and A. T. Hagler, J. Comput. Chem., 16, 154-170 (1995)
Inclusion of Charge and Polarizability Fluxes Provides Needed Physical Accuracy in Molecular Me-
chanics Force Fields, K. Palmo, B. Mannifors, N. G. Mirkin and S. Krimm, Chem. Phys. Lett., 429,
628-632 (2006)
Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential, C.
Liu, J.-P. Piquemal and P. Ren, J. Phys. Chem. Lett., 11, 419-426 (2020)

14.2.15 Analytical Derivatives of Potential Functions

First and Second Derivative Matrix Elements for the Stretching, Bending, and Torsional Energy, K.
J. Miller, R. J. Hinde and J. Anderson, J. Comput. Chem., 10, 63-76 (1989)
Alternative Expressions for Energies and Forces Due to Angle Bending and Torsional Energy, Report
G320-3561, W. C. Swope and D. M. Ferguson, J. Comput. Chem., 13, 585-594 (1992)
New Formulation for Derivatives of Torsion Angles and Improper Torsion Angles in Molecular Me-
chanics: Elimination of Singularities, A. Blondel and M. Karplus, J. Comput. Chem., 17, 1132-1141
(1996)
Efficient Treatment of Out-of-Plane Bend and Improper Torsion Interactions in MM2, MM3, and
MM4 Molecular Mechanics Calculations, R. E. Tuzun, D. W. Noid and B. G. Sumpter, J. Comput.
Chem., 18, 1804-1811 (1997)

272 Chapter 14. References

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14.2.16 Torsional Space Derivatives and Normal Modes

Protein Normal-mode Dynamics: Trypsin Inhibitor, Crambin, Ribonuclease and Lysozyme, M.

Levitt, C. Sander and P. S. Stern, J. Mol. Biol., 181, 423-447 (1985)
Protein Folding by Restrained Energy Minimization and Molecular Dynamics, M. Levitt, J. Mol.
Biol., 170, 723-764 (1983)
Algorithm for Rapid Calculation of Hessian of Conformational Energy Function of Proteins by Su-
percomputer, H. Wako and N. Go, J. Comput. Chem., 8, 625-635 (1987)
Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Di-
hedral Angles for Proteins: General Recurrent Equations, H. Abe, W. Braun, T. Noguti and N. Go,
Computers & Chemistry, 8, 239-247 (1984)
A Method of Rapid Calculation of a Second Derivative Matrix of Conformational Energy for Large
Molecules, T. Noguti and N. Go, J. Phys. Soc. Japan, 52, 3685-3690 (1983)

14.2.17 Analytical Surface Area and Volume

Analytical Molecular Surface Calculation, M. L. Connolly, J. Appl. Cryst., 16, 548-558 (1983)
Computation of Molecular Volume, M. L. Connolly, J. Am. Chem. Soc., 107, 1118-1124 (1985)
Molecular Surfaces: A Review, M. L. Connolly, available from the site https://web.archive.org/
web/20120311082019/http://www.netsci.org/Science/Compchem/feature14.html/
Algorithms for Calculating Excluded Volume and Its Derivatives as a Function of Molecular Confor-
mation and Their Use in Energy Minimization, C. E. Kundrot, J. W. Ponder and F. M. Richards, J.
Comput. Chem., 12, 402-409 (1991)
Solvent Accessible Surface Area and Excluded Volume in Proteins, T. J. Richmond, J. Mol. Biol.,
178, 63-89 (1984)
Atomic Solvation Parameters Applied to Molecular Dynamics of Proteins in Solution, L. Wesson and
D. Eisenberg, Protein Science, 1, 227-235 (1992)
Implementation of Solvent Effect in Molecular Mechanics, Part 3. The First- and Second-order
Analytical Derivatives of Excluded Volume, V. Gononea and E. Osawa, J. Mol. Struct. (Theochem),
311 305-324 (1994)
Geometric Measures of Large Biomolecules: Surface, Volume, and Pockets, P. Mach and P. Koehl, J.
Comput. Chem., 32, 3023-3038 (2011)
Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their
Derivatives, P. Koehl, A. Akopyan and H. Edelsbrunner, J. Chem. Inf. Model, 63, 973-985 (2023)

14.2. Literature References by Topic 273

Tinker User's Guide

14.2.18 Approximate Surface Area and Volume

Analytical Approximation to the Accessible Surface Area of Proteins, S. J. Wodak and J. Janin, Proc.
Natl. Acad. Sci. USA, 77, 1736-1740 (1980)
A Rapid Approximation to the Solvent Accessible Surface Areas of Atoms, W. Hasel, T. F. Hendrick-
son and W. C. Still, Tetrahedron Comput. Method., 1, 103-116 (1988)
Approximate Solvent-Accessible Surface Areas from Tetrahedrally Directed Neighber Densities, J.
Weiser, P. S. Shenkin and W. C. Still, Biopolymers, 50, 373-380 (1999)
Efficient Gaussian Density Formulation of Volume and Surface Areas of Macromolecules on Graph-
ical Processing Units, B. Zhang, D. Kilburg, P. Eastman, V. S. Pande and E. Gallicchio, J. Comput.
Chem., 38, 740-752 (2017)

14.2.19 Boundary Conditions and Neighbor Methods

On Searching Neighbors in Computer Simulations of Macromolecular Systems, W. F. van Gun-

steren, H. J. C. Berendsen, F. Colonna, D. Perahia, J. P. Hollenberg and D. Lellouch, J. Comput.
Chem., 5, 272-279 (1984)
Molecular Dynamics on Vector Computers, F. Sullivan, R. D. Mountain and J. O’Connell, J. Comput.
Phys., 61, 138-153 (1985)
A Vectorized “Near Neighbors” Algorithm of Order N Using a Monotonic Logical Grid, J. Boris, J.
Comput. Phys., 66, 1-20 (1986)
Geometric Properties of the Monotonic Lagrangian Grid Algorithm for Near Neighbors Calculations,
S. G. Lambrakos and J. P. Boris, J. Comput. Phys., 73, 183-202 (1987)
The Role of Long Ranged Forces in Determining the Structure and Properties of Liquid Water, T. A.
Andrea, W. C. Swope and H. C. Andersen, J. Chem. Phys., 79, 4576-4584 (1983)
Geometrical Considerations in Model Systems with Periodic Boundary Conditions, D. N. Theodorou
and U. W. Suter, J. Chem. Phys., 82, 955-966 (1985)
A Hierarchical O(NlogN) Force-calculation Algorithm, J. Barnes and P. Hut, Nature, 234, 446-449
(1986)

14.2.20 Cutoff and Truncation Methods

New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation, P. J. Stein-

bach and B. R. Brooks, J. Comput. Chem., 15, 667-683 (1993)
The Effects of Truncating Long-Range Forces on Protein Dynamics, R. J. Loncharich and B. R.
Brooks, Proteins, 6, 32-45 (1989)
Structural and Energetic Effects of Truncating Long Ranged Interactions in Ionic and Polar Fluids,
C. L. Brooks III, B. M. Pettitt and M. Karplus, J. Chem. Phys., 83, 5897-5908 (1985)

274 Chapter 14. References

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14.2.21 Ewald Summation Techniques

Ewald Summation Techniques in Perspective: A Survey, A. Y. Toukmaji and J. A. Board, Jr., Comp.
Phys. Commun., 95, 73-92 (1996)
New Tricks for Modelers from the Crystallography Toolkit: The Particle Mesh Ewald Algorithm
and its Use in Nucleic Acid Simulations, T. Darden, L. Perera, L. Li and L. Pedersen, Structure, 7,
R550-R60 (1999)
Particle Mesh Ewald: An Nlog(N) Method for Ewald Sums in Large Systems, T. Darden, D. York
and L. G. Pedersen, J. Chem. Phys., 98, 10089-10092 (1993)
A Smooth Particle Mesh Ewald Method, U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee
and L. G. Pedersen, J. Chem. Phys., 103, 8577-8593 (1995)
Point Multipoles in the Ewald Summation (Revisited), W. Smith, CCP5 Newsletter, 46, 18-30
(1998), available at the site https://www.ccp5.ac.uk/infoweb/newsletters/
Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water, S. E. Feller,
R. W. Pastor, A. Rojnuckarin, S. Bogusz and B. R. Brooks, J. Phys. Chem., 100, 17011-17020 (1996)
Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions:
Influence of Artificial Periodicity on Peptide Conformation, W. Weber, P. H. Hunenberger and J. A.
McCammon, J. Phys. Chem. B, 104, 3668-3675 (2000)

14.2.22 Conjugated and Aromatic Systems

Molecular Mechanics (MM3) Calculations on Conjugated Hydrocarbons, N. L. Allinger, F. Li, L. Yan

and J. C. Tai, J. Comput. Chem., 11, 868-895 (1990)
The MMP2 Calculational Method, J. T. Sprague, J. C. Tai, Y. Yuh and N. L. Allinger, J. Comput.
Chem., 8, 581-603 (1987)
A Molecular Orbital Based Molecular Mechanics Approach to Study Conjugated Hydrocarbons, J.
Kao, J. Am. Chem. Soc., 109, 3818-3829 (1987)
Conformational Analysis: Heats of Formation of Conjugated Hydrocarbons by the Force Field
Method, J. Kao and N. L. Allinger, J. Am. Chem. Soc., 99, 975-986 (1977)
Accurate Heats of Atomization and Accurate Bond Lengths: Benzenoid Hydrocarbons, D. H. Lo and
M. A. Whitehead, Can. J. Chem., 46, 2027-2040 (1968)
Hetero-atomic Molecules: Semi-empirical Molecular Orbital Calculations and Prediction of Physical
Properties, G. D. Zeiss and M. A. Whitehead, J. Chem. Soc. A, 1727-1738 (1971)

14.2. Literature References by Topic 275

Tinker User's Guide

14.2.23 Free Energy Simulation Methods

Free Energy Calculations: Applications to Chemical and Biochemical Phenomena, P. Kollman,

Chem. Rev., 93, 2395-2417 (1993)
Ligand-Receptor Interactions, B. L. Tembe and J. A. McCammon, Computers & Chemistry, 8, 281-
283 (1984)
Monte Carlo Simulation of Differences in Free Energy of Hydration, W. L. Jorgensen and C. Ravi-
mohan, J. Chem. Phys., 83, 3050-3054 (1985)
Efficient Computation of Absolute Free Energies of Binding by Computer Simulations: Application
to the Methane Dimer in Water, W. L. Jorgensen, J. K. Buckner, S. Boudon and J. Tirado-Rives, J.
Chem. Phys., 89, 3742-3746 (1988)
Thermodynamics of Aqueous Solvation: Solution Properties of Alcohols and Alkanes, S. H. Fleis-
chman and C. L. Brooks III, J. Chem. Phys., 87, 3029-3037 (1987)
An Approach to the Application of Free Energy Perturbation Methods Using Molecular Dynamics,
U. C. Singh, F. K. Brown, P. A. Bash and P. A. Kollman, J. Am. Chem. Soc., 109, 1607-1614 (1987)
A New Method for Carrying out Free Energy Perturbation Calculations: Dynamically Modified Win-
dows, D. A. Pearlman and P. A. Kollman, J. Chem. Phys., 90, 2460-2470 (1989)
Free Energy of Hydrophobic Hydration: A Molecular Dynamics Study of Noble Gases in Water, T.
P. Straatsma, H. J. C. Berendsen and J. P. M. Postma, J. Chem. Phys., 85, 6720-6727 (1986)
Free Energy of Ionic Hydration: Analysis of a Thermodynamic Integration Technique to Evaluate
Free Energy Differences by Molecular Dynamics Simulations, T. P. Straatsma and H. J. C. Berend-
sen, J. Chem. Phys., 89, 5876-5886 (1988)
The Finite Difference Thermodynamic Integration, Tested on Calculating the Hydration Free Energy
Difference between Acetone and Dimethylamine in Water, M. Mezei, J. Chem. Phys., 86, 7084-7088
(1987)
Decomposition of the Free Energy of a System in Terms of Specific Interactions, A. E. Mark and W.
F. van Gunsteren, J. Mol. Biol., 240, 167-176 (1994)
The Meaning of Copmponent Analysis: Decomposition of the Free Energy in Terms of Specific
Interactions, S. Boresch and M. Karplus, J. Mol. Biol., 254, 801-807 (1995)

14.2.24 Methods for Parameter Determination

Molecular Mechanics Parameters, N. L. Allinger, X. Zhou and J. Bergsma, J. Mol. Struct.

(THEOCHEM), 312, 69-83 (1994)
The Atom-Atom Potential Method: Application to Organic Molecular Solids, A. J. Pertsin and A. I.
Kitaigorodsky, Springer-Verlag, Berlin, 1987
Transferable Empirical Nonbonded Potential Functions, D. E. Williams, in Crystal Cohesion and
Conformational Energies, Ed. by R. M. Metzger, Springer-Verlag, Berlin, 1981
A Procedure for Obtaining Energy Parameters from Crystal Packing, A. T. Hagler and S. Lifson, Acta
Cryst., B30, 1336-1341 (1974)

276 Chapter 14. References

 Tinker User's Guide

Consistent Force Field Studies of Intermolecular Forces in Hydrogen-Bonded Crystals: A Benchmark

for the Objective Comparison of Alternative Force Fields, A. T. Hagler, S. Lifson and P. Dauber, J.
Am. Chem. Soc., 101, 5122-5130 (1979)
Optimized Intermolecular Potential Functions for Liquid Hydrocarbons, W. L. Jorgensen, J. D.
Madura and C. J. Swenson, J. Am. Chem. Soc., 106, 6638-6646 (1984)
Optimized Intermolecular Potential Functions for Amides and Peptides: Structure and Properties of
Liquid Amides, W. L. Jorgensen and C. J. Swenson, J. Am. Chem. Soc., 107, 569-578 (1985)
Derivation of Force Fields for Molecular Mechanics and Dynamics from ab Initio Surfaces, J. R.
Maple, U. Dinur and A. T. Hagler, Proc. Nat. Acad. Sci. USA, 85, 5350-5354 (1988)
Direct Evaluation of Nonbonding Interactions from ab Initio Calculations, U. Dinur and A. T. Hagler,
J. Am. Chem. Soc., 111, 5149-5151 (1989)

14.2.25 Electrostatic Interactions

Towards More Accurate Model Intermolecular Potentials for Organic Molecules, S. L. Price, Rev.
Comput. Chem., 14, 225-289 (2000)
A Transferable Distributed Multipole Model for the Electrostatic Interactions of Peptides and
Amides, C. H. Faerman and S. L. Price, J. Am. Chem. Soc., 112, 4915-4926 (1990)
Electrostatic Interaction Potentials in Molecular Force Fields, C. E. Dykstra, Chem. Rev., 93, 2339-
2353 (1993)
Accurate Modeling of the Intramolecular Electrostatic Energy of Proteins, M. J. Dudek and J. W.
Ponder, J. Comput. Chem., 16, 791-816 (1995)
An Improved Description of the Molecular Charge Density in Force Fields with Atomic Multipole
Moments, U. Koch and E. Egert, J. Comput. Chem., 16, 937-944 (1995)
Representation of the Molecular Electrostatic Potential by Atomic Multipole and Bond Dipole Mod-
els, D. E. Williams, J. Comput. Chem., 9, 745-763 (1988)
Critical Analysis of Electric Field Modeling: Formamide, F. Colonna, E. Evleth and J. G. Angyan, J.
Comput. Chem., 13, 1234-1245 (1992)

14.2.26 Polarization Effects

Incorporating Electric Polarizabilities in Water-Water Interaction Potentials, S. Kuwajima and A.

Warshel, J. Phys. Chem., 94, 460-466 (1990)
Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol,
and N-Methylacetamide, J. W. Caldwell and P. A. Kollman, J. Phys. Chem., 99, 6208-6219 (1995)
An Anisotropic Polarizable Water Model: Incorporation of All-Atom Polarizabilities into Molecular
Mechanics Force Fields, D. N. Bernardo, Y. Ding, K. Kroegh-Jespersen and R. M. Levy, J. Phys.
Chem., 98, 4180-4187 (1994)
Molecular and Atomic Polarizabilities: Thole’s Model Revisited, P. T. van Duijnen and M. Swart, J.
Phys. Chem. A, 102, 2399-2407 (1998)

14.2. Literature References by Topic 277

Tinker User's Guide

Calculation of the Molecular Polarizability Tensor, K. J. Miller, J. Am. Chem. Soc., 112, 8543-8551
(1990)
An Atom Dipole Interaction Model for Molecular Polarizability. Application to Polyatomic Molecules
and Determination of Atom Polarizabilities, J. Applequist, J. R. Carl and K.-K. Fung, J. Am. Chem.
Soc., 94, 2952-2960 (1972)
Atom Charge Transfer in Molecular Polarizabilities. Application of the Olson-Sundberg Model to
Aliphatic and Aromatic Hydrocarbons, J. Applequist, J. Phys. Chem., 97, 6016-6023 (1993)
Distributed Polarizabilities, A. J. Stone, Mol. Phys., 56, 1065-1082 (1985)
A Distributed Model of the Electrical Response of Organic Molecules, J. M. Stout and C. E. Dykstra,
J. Phys. Chem. A, 102, 1576-1582 (1998)

14.2.27 Macroscopic Treatment of Solvent

Continuum Solvation Models: Classical and Quantum Mechanical Implementations, C. J. Cramer

and D. G. Truhlar, Rev. Comput. Chem., 6, 1-72 (1995)
Implicit Solvation Models, B. Roux and T. Simonson, Biophys. Chem., 78, 1-20 (1999)
Introduction to Continuum Electrostatics with Molecular Applications, M. K. Gilson, available at
the site http://gilsonlab.umbi.umd.edu/

14.2.28 Surface Area-Based Solvation Models

Solvation Energy in Protein Folding and Binding, D. Eisenberg and A. D. McLachlan, Nature, 319,
199-203 (1986)
Atomic Solvation Parameters Applied to Molecular Dynamics of Proteins in Solution, L. Wesson and
D. Eisenberg, Prot. Sci., 1, 227-235 (1992)
Accessible Surface Areas as a Measure of the Thermodynamic Parameters of Hydration of Peptides,
T. Ooi, M. Oobatake, G. Nemethy and H. A. Scheraga, Proc. Natl. Acad. Sci. USA, 84, 3086-3090
(1987)
An Efficient, Differentiable Hydration Potential for Peptides and Proteins, J. D. Augspurger and H.
A. Scheraga, J. Comput. Chem., 17, 1549-1558 (1996)

14.2.29 Generalized Born Solvation Models

A Semiempirical Treatment of Solvation for Molecular Mechanics and Dynamics, W. C. Still, A.

Tempczyk, R. C. Hawley and T. Hendrickson, J. Am. Chem. Soc., 112, 6127-6129 (1990)
The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Ap-
proximate Born Radii, D. Qiu, P. S. Shenkin, F. P. Hollinger and W. C. Still, J. Phys. Chem. A, 101,
3005-3014 (1997)
Pairwise Solute Descreening of Solute Charges from a Dielectric Medium, G. D. Hawkins, C. J.
Cramer and D. G. Truhlar, Chem. Phys. Lett., 246, 122-129 (1995)

278 Chapter 14. References

 Tinker User's Guide

Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of So-
lute Atomic Charges from a Dielectric Medium, G. D. Hawkins, C. J. Cramer and D. G. Truhlar, J.
Phys. Chem., 100, 19824-19839 (1996)
Modification of the Generalized Born Model Suitable for Macromolecules, A. Onufriev, D. Bashford
and D. A. Case, J. Phys. Chem. B, 104, 3712-3720 (2000)
A Comprehensive Analytical Treatment of Continuum Electrostatics, M. Schaefer and M. Karplus,
J. Phys. Chem., 100, 1578-1599 (1996)
Solution Conformations and Thermodynamics of Structured Peptides: Molecular Dynamics Simu-
lation with an Implicit Solvation Model, M. Schaefer, C. Bartels and M. Karplus, J. Mol. Biol., 284,
835-848 (1998)

14.2.30 Superposition of Coordinate Sets

An Algorithm for the Simultaneous Superposition of a Structural Series, S. J. Kearsley, J. Comput.

Chem., 11, 1187-1192 (1990)
A Note on the Rotational Superposition Problem, R. Diamond, Acta Cryst., A44, 211-216 (1988)
Rapid Comparison of Protein Structures, A. D. McLachlan, Acta Cryst., A38, 871-873 (1982)
Some Uses of a Best Molecular Fit Routine, S. C. Nyburg, Acta Cryst., B30, 251-253 (1974)

14.2.31 Location of Transition States

Reaction Path Study of Conformational Transitions and Helix Formation in a Tetrapeptide, R. Czer-
minski and R. Elber, Proc. Nat. Acad. Sci. USA, 86, 6963 (1989)
Finding Saddles on Multidimensional Potential Surfaces, R. S. Berry, H. L. Davis and T. L. Beck,
Chem. Phys. Lett., 147, 13 (1988)
Reaction Paths on Multidimensional Energy Hypersurfaces, K. Muller, Ang. Chem. Int. Ed. Engl.,
19, 1-13 (1980)
Locating Transition States, S. Bell and J. S. Crighton, J. Chem. Phys., 80, 2464-2475 (1984)
Conjugate Peak Refinement: An Algorithm for Finding Reaction Paths and Accurate Transition
States in Systems with Many Degrees of Freedom, S. Fischer and M. Karplus, Chem. Phys. Lett.,
194, 252-261 (1992)
A New Method of Saddle-Point Location for the Calculation of Defect Migration Energies, J. E.
Sinclair and R. Fletcher, J. Phys. C, 7, 864-870 (1974)
A Method for Determining Reaction Paths in Large Molecules: Application to Myoglobin, R. Elber
and M. Karplus, Chem. Phys. Lett., 139, 375-380 (1987)
On Finding Stationary States on Large-Molecule Potential Energy Surfaces, D. T. Nguyen and D. A.
Case, J. Phys. Chem., 89, 4020-4026 (1985)
The Synchronous-Transit Method for Determining Reaction Pathways and Locating Molecular Tran-
sition States, T. A. Halgren and W. N. Lipscomb, Chem. Phys. Lett., 49, 225-232 (1977)

14.2. Literature References by Topic 279

Tinker User's Guide

Event-Based Relaxation of Continuous Disordered Systems, G. T. Barkema and N. Mousseau, Phys.

Rev. Lett., 77, 4358-4361 (1996)

280 Chapter 14. References

 INDEX

A APBS-FGCENT, 59
A-AXIS, 54 APBS-FGRID, 59
A-EXPTERM, 54 APBS-GCENT, 59
ACTIVE, 54 APBS-GRID, 59
ACTIVE-SPHERE, 54 APBS-ION, 59
ALF-METHOD, 54 APBS-MG-AUTO, 60
ALF-NOHYDRO, 55 APBS-MG-MANUAL, 60
ALF-SORT, 55 APBS-PDIE, 60
ALF-SOSGMP, 55 APBS-RADII, 60
ALPHA, 55 APBS-SDENS, 60
ANGANG, 55 APBS-SDIE, 60
ANGANGTERM, 55 APBS-SMIN, 60
ANGANGUNIT, 55 APBS-SRAD, 60
ANGCFLUX, 55 APBS-SRFM, 60
ANGLE, 56 APBS-SWIN, 61
ANGLE3, 56 ARCHIVE, 61
ANGLE4, 57 ATOM, 61
ANGLE5, 57 AUX-TAUTEMP, 61
ANGLE-CUBIC, 56 AUX-TEMP, 61
ANGLE-PENTIC, 56
ANGLE-QUARTIC, 56
B
ANGLE-SEXTIC, 56 B-AXIS, 61
ANGLEF, 57 B-EXPTERM, 61
ANGLEP, 57 BAROSTAT, 61
ANGLETERM, 58 BASIN, 61
ANGLEUNIT, 58 BEEMAN-MIXING, 62
ANGMAX, 58 BETA, 62
ANGTORS, 58 BIOTYPE, 62
ANGTORTERM, 58 BOND, 62
ANGTORUNIT, 58 BOND3, 62
ANISO-PRESSURE, 58 BOND4, 63
APBS-AGRID, 59 BOND5, 63
APBS-BCFL, 59 BOND-CUBIC, 62
APBS-CGCENT, 59 BOND-QUARTIC, 62
APBS-CGRID, 59 BONDTERM, 63
APBS-CHGM, 59 BONDTYPE, 63
APBS-DIME, 59 BONDUNIT, 63

281
Tinker User's Guide

BORN-RADIUS, 63 DIFFUSE-VDW, 68
DIGITS, 68
C DIPOLE, 69
C-AXIS, 64 DIPOLE3, 69
C-EXPTERM, 64 DIPOLE4, 69
CAPPA, 64 DIPOLE5, 70
CAVITY-PROBE, 64 DIPOLE-CUTOFF, 69
CHARGE, 64 DIPOLE-TAPER, 69
CHARGE-CUTOFF, 64 DIPOLETERM, 70
CHARGE-LIST, 64 DIRECT-11-SCALE, 70
CHARGE-TAPER, 64 DIRECT-12-SCALE, 70
CHARGETERM, 64 DIRECT-13-SCALE, 70
CHARGETRANSFER, 65 DIRECT-14-SCALE, 70
CHG-11-SCALE, 65 DISP-12-SCALE, 70
CHG-12-SCALE, 65 DISP-13-SCALE, 70
CHG-13-SCALE, 65 DISP-14-SCALE, 71
CHG-14-SCALE, 65 DISP-15-SCALE, 71
CHG-15-SCALE, 65 DISP-CORRECTION, 71
CHG-BUFFER, 65 DISP-CUTOFF, 71
CHGDPLTERM, 65 DISP-LIST, 71
CHGFLXTERM, 65 DISP-TAPER, 71
CHGPEN, 66 DISPERSION, 71
CHGTRN, 66 DISPERSIONTERM, 71
CHGTRN-CUTOFF, 66 DIVERGE, 72
CHGTRN-TAPER, 66 DODECAHEDRON, 72
CHGTRNTERM, 66 DPME-GRID, 72
COLLISION, 66 DPME-ORDER, 72
COMPRESS, 66
CUDA-DEVICE, 66 E
CUTOFF, 67 ECHO, 72
ELE-LAMBDA, 72
D ELECTNEG, 72
D-EQUALS-P, 67 ELECTRIC, 72
DCD-ARCHIVE, 67 ENFORCE-CHIRALITY, 73
DEBUG, 67 EPSILONRULE, 73
DEFORM, 67 EWALD, 73
DEGREES-FREEDOM, 67 EWALD-ALPHA, 73
DELCX-EPS, 67 EWALD-BOUNDARY, 73
DELTA-HALGREN, 67 EWALD-CUTOFF, 73
DESCREEN-HYDROGEN, 68 EXCHANGE-POLAR, 73
DESCREEN-OFFSET, 68 EXCHPOL, 74
DEWALD, 68 EXIT-PAUSE, 74
DEWALD-ALPHA, 68 EXTERNAL-FIELD, 73
DEWALD-CUTOFF, 68 EXTRATERM, 74
DIELECTRIC, 68
DIELECTRIC-OFFSET, 68 F
DIFFUSE-CHARGE, 68 FCTMIN, 74
DIFFUSE-TORSION, 68 FFT-PACKAGE, 74

282 Index
 Tinker User's Guide

FIT-ANGLE, 74 IMPTORS, 78
FIT-BOND, 74 IMPTORSTERM, 78
FIT-OPBEND, 74 IMPTORSUNIT, 78
FIT-STRBND, 74 INACTIVE, 78
FIT-TORSION, 74 INDUCE-12-SCALE, 78
FIT-UREY, 74 INDUCE-13-SCALE, 78
FIX-ANGLE, 74 INDUCE-14-SCALE, 79
FIX-ATOM-DIPOLE, 74 INDUCE-15-SCALE, 79
FIX-BOND, 74 INTEGRATOR, 79
FIX-CHGPEN, 74 INTMAX, 79
FIX-DIPOLE, 75
FIX-MONOPOLE, 75 L
FIX-OPBEND, 75 LAMBDA, 79
FIX-QUADRUPOLE, 75 LBFGS-VECTORS, 79
FIX-STRBND, 75 LIGAND, 79
FIX-TORSION, 75 LIGHTS, 79
FIX-UREY, 75 LIST-BUFFER, 80
FORCEFIELD, 75
FRICTION, 75 M
FRICTION-SCALING, 75 MAXITER, 80
METAL, 80
G METALTERM, 80
GAMMA, 75 MMFF-PIBOND, 80
GAMMA-HALGREN, 76 MMFFANGLE, 80
GAMMAMIN, 76 MMFFAROM, 80
GAUSSTYPE, 76 MMFFBCI, 80
GK-RADIUS, 76 MMFFBOND, 80
GKC, 76 MMFFBONDER, 80
GKR, 76 MMFFCOVRAD, 80
GROUP, 76 MMFFDEFSTBN, 80
GROUP-INTER, 76 MMFFEQUIV, 80
GROUP-INTRA, 76 MMFFOPBEND, 80
GROUP-MOLECULE, 76 MMFFPBCI, 80
GROUP-SELECT, 76 MMFFPROP, 80
MMFFSTRBND, 80
H MMFFTORSION, 80
HBOND, 77 MMFFVDW, 80
HCT-ELEMENT, 77 MPOLE-12-SCALE, 80
HCT-SCALE, 77 MPOLE-13-SCALE, 81
HEAVY-HYDROGEN, 77 MPOLE-14-SCALE, 81
HESSIAN-CUTOFF, 77 MPOLE-15-SCALE, 81
HGUESS, 77 MPOLE-CUTOFF, 81
MPOLE-LIST, 81
I MPOLE-TAPER, 81
IEL-SCF, 77 MULTIPOLE, 81
IMPROPER, 77 MULTIPOLETERM, 82
IMPROPTERM, 77 MUTATE, 82
IMPROPUNIT, 78 MUTUAL-11-SCALE, 82

Index 283
Tinker User's Guide

MUTUAL-12-SCALE, 82 PIATOM, 87
MUTUAL-13-SCALE, 82 PIBOND, 87
MUTUAL-14-SCALE, 82 PIBOND4, 87
PIBOND5, 87
N PISYSTEM, 87
NECK-CORRECTION, 82 PITORS, 87
NEIGHBOR-GROUPS, 82 PITORSTERM, 87
NEIGHBOR-LIST, 83 PITORSUNIT, 88
NEUTRAL-GROUPS, 83 PME-GRID, 88
NEWHESS, 83 PME-ORDER, 88
NEXTITER, 83 POLAR-12-INTRA, 88
NOARCHIVE, 83 POLAR-12-SCALE, 88
NODESCREEN, 83 POLAR-13-INTRA, 88
NONBONDTERM, 83 POLAR-13-SCALE, 88
NOSYMMETRY, 83 POLAR-14-INTRA, 88
NOVERSION, 83 POLAR-14-SCALE, 88
POLAR-15-INTRA, 88
O POLAR-15-SCALE, 89
OCTAHEDRON, 84 POLAR-EPS, 89
ONION-PROBE, 84 POLAR-ITER, 89
OPBEND, 84 POLAR-PREDICT, 89
OPBEND-CUBIC, 84 POLARIZABLE, 89
OPBEND-PENTIC, 84 POLARIZATION, 89
OPBEND-QUARTIC, 84 POLARIZE, 89
OPBEND-SEXTIC, 84 POLARIZETERM, 90
OPBENDTERM, 85 POLPAIR, 90
OPBENDTYPE, 85 POLYMER-CUTOFF, 90
OPBENDUNIT, 85 POTENTIAL-ATOMS, 90
OPDIST, 85 POTENTIAL-FACTOR, 90
OPDIST-CUBIC, 85 POTENTIAL-FIT, 90
OPDIST-PENTIC, 85 POTENTIAL-OFFSET, 90
OPDIST-QUARTIC, 86 POTENTIAL-SHELLS, 90
OPDIST-SEXTIC, 86 POTENTIAL-SPACING, 90
OPDISTTERM, 86 PPME-ORDER, 91
OPDISTUNIT, 86 PRINTOUT, 91
OPENMP-THREADS, 86
OPT-COEFF, 86 R
OVERWRITE, 86 RADIUSRULE, 91
RADIUSSIZE, 91
P RADIUSTYPE, 91
PARAMETERS, 86 RANDOMSEED, 91
PCG-GUESS, 87 RATTLE, 91
PCG-NOGUESS, 87 RATTLE-DISTANCE, 91
PCG-NOPRECOND, 87 RATTLE-EPS, 92
PCG-PEEK, 87 RATTLE-LINE, 92
PCG-PRECOND, 87 RATTLE-ORIGIN, 92
PENETRATION, 87 RATTLE-PLANE, 92
PEWALD-ALPHA, 87 REACTIONFIELD, 92

284 Index
 Tinker User's Guide

REDUCE, 92 T
REMOVE-INERTIA, 92 TANH-CORRECTION, 98
REP-12-SCALE, 92 TAPER, 98
REP-13-SCALE, 92 TARGET-DIPOLE, 98
REP-14-SCALE, 92 TARGET-QUADRUPOLE, 98
REP-15-SCALE, 92 TAU-PRESSURE, 98
REPULS-CUTOFF, 92 TAU-TEMPERATURE, 98
REPULS-TAPER, 93 TCG-GUESS, 98
REPULSION, 93 TCG-NOGUESS, 98
REPULSIONTERM, 93 TCG-PEEK, 98
RESP-WEIGHT, 93 THERMOSTAT, 98
RESPA-INNER, 93 TORS-LAMBDA, 98
RESPTYPE, 93 TORSION, 98
RESTRAIN-ANGLE, 93 TORSION4, 99
RESTRAIN-DISTANCE, 93 TORSION5, 99
RESTRAIN-GROUPS, 94 TORSIONTERM, 99
RESTRAIN-PLANE, 94 TORSIONUNIT, 99
RESTRAIN-POSITION, 94 TORTORS, 99
RESTRAIN-TORSION, 94 TORTORTERM, 99
RESTRAINTERM, 95 TORTORUNIT, 99
ROTATABLE-BOND, 95 TRIAL-DISTANCE, 100
RXNFIELDTERM, 95 TRIAL-DISTRIBUTION, 100
TRUNCATE, 100
S
SADDLEPOINT, 95 U
SAVE-CYCLE, 95 UNWRAP-COORDS, 100
SAVE-FORCE, 95 UREY-CUBIC, 100
SAVE-INDUCED, 95 UREY-QUARTIC, 100
SAVE-VECTS, 95 UREYBRAD, 100
SAVE-VELOCITY, 95 UREYTERM, 100
SLOPEMAX, 95 UREYUNIT, 101
SMOOTHING, 96 USOLVE-ACCEL, 101
SOLUTE, 96 USOLVE-BUFFER, 101
SOLVATE, 96 USOLVE-CUTOFF, 101
SOLVATETERM, 96 USOLVE-DIAGONAL, 101
SOLVENT-PRESSURE, 96 USOLVE-LIST, 101
SPACEGROUP, 96
STEEPEST-DESCENT, 96 V
STEPMAX, 96 VALENCETERM, 101
STEPMIN, 97 VDW, 101
STRBND, 97 VDW14, 103
STRBNDTERM, 97 VDW-12-SCALE, 101
STRBNDUNIT, 97 VDW-13-SCALE, 102
STRTORS, 97 VDW-14-SCALE, 102
STRTORTERM, 97 VDW-15-SCALE, 102
STRTORUNIT, 97 VDW-ANNIHILATE, 102
SURFACE-TENSION, 98 VDW-CORRECTION, 102
VDW-CUTOFF, 102

Index 285
Tinker User's Guide

VDW-LAMBDA, 102
VDW-LIST, 102
VDW-TAPER, 103
VDWINDEX, 103
VDWPAIR, 103
VDWTERM, 103
VDWTYPE, 103
VERBOSE, 103
VIB-ROOTS, 103
VIB-TOLERANCE, 103
VOLUME-MOVE, 103
VOLUME-SCALE, 104
VOLUME-TRIAL, 104

W
WALL, 104
WRAP-COORDS, 104
WRITEOUT, 104

X
X-AXIS, 104

Y
Y-AXIS, 104

Z
Z-AXIS, 104

286 Index