Gwangju Institute of Science and Technology (GIST)

Super Computing & Collaboration Environment Technology Center (SCENT)

LAMMPS for Molecular Dynamics Simulation

Taekhee Ryu
Molecular Modeling Laboratory (MML)
School of Materials Science and Engineering (MSE)
Gwangju Institute of Science and Technology (GIST)

Overview: What is LAMMPS

Lesson 1: Preparing input file
Lesson 2: Running LAMMPS
Lesson 3: Viewing output file

What is LAMMPS
Large-scale Atomic/Molecular Massively Parallel Simulation
- By Dr. S. Plimpton (http://lammps.dandia.gov)
Free open-source code (C++)
Model System with only a few particles up to millions or billions
(depends on computational power)

Designed for Parallel applications

Capable for Atomic, polyatomic, biological, metallic, granular system

LAMMPS doesnt
Build Molecular systems
Use a builder code or write out your own config file
Can build lattices, grain boundaries, etc

Assign force-field coefficients auto-magically

Only hard for molecules, use another MD code

Compute lots of diagnostics on-the-fly

Often better left to post-processing

Visualize your output

Many packages do this
VMD, Rasmol, AtomEye, Ensight,..

Overview of LAMMPS simulation

INPUT

(log.***, dump.***)

OUTPUT

RUNNING

INPUT

(**.cmd, in.**, data.**)

- Initial positions
and velocities
- Boundary
conditions
- Potential energy
function
- Etc.

OUTPUT

RUNNING

Molecular
Dynamics
Simulation

- Trajectories
- Forces
- Energy of the
system
- Temperature
- Pressure
- etc.

LAMMPS Input

Reads an input script (ASCtext)

One command per line

Command name + arguments (in.***)

Data files(typical components) (data.***)

atom_style
read_data
fix
run

molecular
water.data
1 all nve
10000

Summary of molecular connectivity

Cell dimensions
Force field parameters(pair, bond, angle, dihedral, improper)
Atom info (molecule #, atom type #, charge, xyz coordinates)
Bond info (bonds, angles, etc)

Examples sub-dir has many input scripts

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Example Problems in LAMMPS

Crack:

crack growth in a LJ crystal (2d)

Flow:

couette/poisseuille flow between walls (2d)

Friction:

rubbing of 2 irregular surfaces (2d)

Indent:

crystal response to spherical indenter (2d)

Melt:

rapid melt of 3d LJ system

Micelle:

self-assembly of tiny lipid molecules (2d)

Min:

energy minimization of LJ melt (2d)

Obstacle:

flow around obstacles (2d)

Peptide:

granular particle pour and flow (2d/3d)

Shear:

shear of a metal slab with void (quasi-3d)

Peptide:

dynamics of a small solvated peptide chain (5-mer)

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Hand-on exercise
Download the files
Xming (http://m.vaslor.net/tech/xming)
VMD (http://www.ks.uiuc.edu/Research/vmd/)
Topology file (data.peptide)
Executable file (lammps_kigi.cmd)
Install the programs
Xming
VMD

Hands-on excises (Linux basic)

Connect to the GIST supercomputer (KIGI) using PLSI portal
software
Visit PLSI Portal (http://portal.plsi.or.kr)

http://portal.plsi.or.kr

Downloads the PORTAL software for your platform

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1. Extract the files from archive (*.zip)

2. Execute the file
- plsi.exe (Windows)
- plsi
(Mac)

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Sign in
- Enter your account information

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Select

Click the right mouse button

and click the (A)

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Connected to PLSI login node with SSH terminal

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Hand-on exercise
Connect to the GIST supercomputer (kigi)
$ ssh kigi-lg01

connect to the kigi

$ mkdir test1

making the directory

$ cd test1

change the directory

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Hand-on exercise
Lammps_kigi.cmd -> executable file
Job name
Error message
Job-time

Input file

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Input script

Full-atom model of 5-mer Metenkaphalin

CHARMM force-field
PPPM Coulombics
SHAKE bond/angle constraints
2 fmsec timestep
Options to play with:
Timestep size

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Input script
1. initialization

2. Atom definition

3. Settings

4. Run a simulation

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Input script - initialization

1. initialization

Set parameters that need to be defined before atom

s are created or read-in from a file
Unit, dimension, newton, processors, boundary, ato
m style, atom modify

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Input script - initialization

Units
1. initialization
sets the style of units used for a simulation
Beginning of an input script
lj, real, metal, si, cgs, electron

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Input script - initialization

1. initialization
atom_style
Define what style of atoms to use in a simulation
Beginning of an input script

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Input script - initialization

1. initialization

2. Atom definition
Boundary - set the style of boundaries for the global simula
tion box in each dimension
3. Settings
Processors - Specify how processors are mapped as a 3d log
ical grid to the global simulation box
Dimension - Set the dimensionality of the simulation. By def
ault LAMMPS runs 3d simulations.

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Input script - initialization

1. initialization

2. Atom definition

pair_style
set the formula uses to compute pairwise interactions
3. Settings

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Input script - initialization

r
1. initialization

2. Atom definition
bond_style
uses to compute bond interactions between pairs of atoms
3. Settings

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Input script - initialization

1. initialization

2. Atom definition
angle_style
uses to compute angle interactions between triplets of atoms
3. Settings

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Input script - initialization

1. initialization

2. Atom definition
dihedral_style
uses to compute dihedral interactions between quadruplets of
atoms
3. Settings

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Input script - initialization

1. initialization

2. Atom definition
improper_style
uses to compute dihedral interactions between quadruplets of
atoms

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Input script - initialization

1. initialization

2. Atom definition

kspace_style
Define a K-space solver for LAMMPS to use each timestep t
o compute long-range Coulombic interactions or long-rang
e 1/r^N interactions
Style none or ewald or pppm or pppm/cg or
The pppm style invokes a particle-particle particle-mesh sol
ver (Hockney) which maps atom charge to a 3d mesh, uses
3d FFTs to solve Poisson's equation on the mesh, then inter
polates electric fields on the mesh points back to the atoms

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Input script - atom definition

1. initialization

2. Atom definition
Read them in from a data or restart file
via the read data or read restart command
3. Settings
Contain molecular topology information
Create atoms on a lattice
with no molecular topology
Lattice, region, create box, create atoms

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Input script
Read_data - Read in a data file containing information L
AMMPS needs to run a simulation (data.***)
1. initialization

# of components
in system

Simulation box
boundaries

Mass

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Input script
Read_data - Read in a data file containing information L
AMMPS needs to run a simulation (data.***)
1. initialization

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Input script
Read_data - Read in a data file containing information L
AMMPS needs to run a simulation (data.***)
1. initialization

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Input script
Read_data - Read in a data file containing information L
AMMPS needs to run a simulation (data.***)
1. initialization

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Input script
Read_data - Read in a data file containing information L
AMMPS needs to run a simulation (data.***)
1. initialization

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Input script
Read_data - Read in a data file containing information L
AMMPS needs to run a simulation (data.***)
1. initialization

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Input script
Charge,

X,

X,

Y,

type,

i,

type,

i,

j,

Y,

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type,

i,

j,

k,

type,

i,

j,

k,

Input script - atom definition

read_data - Read in a data file containing information
LAMMPS needs to run a simulation (data.***)
1. initialization
2. Atom definition

read_restart - Read in a previously saved simulation

from a restart file

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Input script - atom definition

Create atoms on a lattice
with no molecular topology
Lattice, region, create box, create atoms
Lattice
simply a set of points in space
determined by a unit cell with basis atoms
used to define a wide variety of crystallographic
lattices
syntax
example

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Input script - atom definition

Create atoms on a lattice
with no molecular topology
Lattice, region, create box, create atoms
region
This command defines a geometric region of
space
create box
This command creates a simulation box based on
the specified region
create atoms
This command creates atoms on a lattice, or a
single atom, or a random collection of atoms

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Input script - settings

1. initialization

2. Atom definition

3. Settings

3. Run a simulation

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Input script - settings

neighbor
This command sets parameters that affect the bui
lding of pairwise neighbor lists
The style value selects what algorithm is used to
build the list
The bin style creates the list by binning which is
an operation that scales linearly with N/P, the nu
mber of atoms per processor where N = total nu
mber of atoms and P = number of processors

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Input script - settings

Neigh_modify
This command sets parameters that affect the
building and use of pairwise neighbor lists
The delay setting means never build a new list
until at least N steps after the previous build

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Input script - settings

timestep
Set the timestep size for subsequent molecular
dynamics simulations

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Input script - settings

thermo_style
Set the style and content for printing thermodyna
mic data to the screen and log file.
Style multi prints a multiple-line listing of thermo
dynamic info
thermo_style custom etotal ke temp pe ebond ea
ngle edihed eimp evdwl ecoul elong press

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Input script - settings

thermo
Compute and print thermodynamic info on timeste
ps that are a multiple of N and at the beginning an
d end of a simulation

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Input script - settings

fix
Set a fix that will be applied to a group of atoms

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Input script - settings

fix
Set a fix that will be applied to a group of atoms

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Input script - settings

group
Identify a collection of atoms as belonging to a gr
oup
The example above adds all atoms with IDs from 1
to 12 to the group named peptide type

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Input script - settings

dump
snapshot of atom quantities to one or more files ev
ery N timesteps in one of several styles

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Input script
1. initialization

2. Atom definition

3. Settings
run
Run or continue dynamics for a specified number o
f timesteps
3. Run a simulation

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Hand-on exercise
Example-1

Full-atom model of 5-mer Metenkaphalin

CHARMM force-field
PPPM Coulombics
SHAKE bond/angle constraints
2 fmsec timestep
Options to play with:
Timestep size

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Hand-on exercise
Example-2

3d LJ solid
Periodic in x, y, z
Melt an fcc lattice
Options to play with: tempe
rature,
fix nvt or npt

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Hand-on exercise
Running LAMMPS on PLSI supercomputer
$ llsubmit lammps_kigi.cmd

# submit the job

$ llcancel job_id

# cancel the job

$ llq

# job status

$ llstatus

# system status

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Output
There are two basic types of LAMMPS output.
1. Thermodynamic output (log.***)
1. A list of quantities printed every few time steps to the scr
een and log file
2. Dump files (dump.***)
1. Snapshots of atoms and various per-atom values and are
written at a specified frequency.
2. Default format is simple : id, type, x, y, z
3. VMD, Rasmol, AtomEye, XMOVIE

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 Example-1 (log.lammps)

Output

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 Example-2 (log.lammps)

Output

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Visualizer
AtomEye - http://li.mit.edu/Archive/Graphics/A
Rasmol - http://www.umass.edu/microbio/rasmol/
XMOVIE
Auxiliary tool distributed with LAMMPS
Very fast, simple viz
2d projection of 3d systems
/home01/applic/lammps/lammps-18Apr10/intel/ssh/tools
/xmovie/xmovie scale dump.***
VMD - http://www.ks.uiuc.edu/Research/vmd/
Windows, Linux, MacOS X
3d hi-quality viz

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Additional tools
Amber2lmp

AMBER <-> LAMMPS

Binary2txt

binary dump file -> ASC test files

Ch2lmp

CHARMM <-> LAMMPS

Chain

create the chains and solvent

Lmp2arc

LAMMPS -> Accelryss insight MD

Lamp2cfg

LAMMPS -> AtomEYE(*.cfg)

Lmp2vmd

LAMMPS -> VMD

Msi2lmp

LAMMPS -> Accelryss insight MD

Python, micelle2d, matlab, ipp, emacs, eff, eam database, data

2xmovie, creatatoms

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Thank you

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Hand-on exercise
Connect to the GIST supercomputer (kigi)

localhost:0.0

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Hand-on exercise
Connect to the GIST supercomputer (kigi)

Check_use system colours

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Hand-on exercise
Connect to the GIST supercomputer (kigi)

Login01.plsi.or.kr, Port-22

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