This document provides an overview of a course on molecular simulations. The course will cover topics like classical statistical mechanics, Monte Carlo and molecular dynamics simulations, modeling of molecules using different potentials, and techniques like free energy calculations and phase equilibrium simulations. Students will be expected to write simulation programs in languages like Fortran, C or C++. The course will be graded based on assignments, projects, mid-semester and end-semester exams. Molecular simulation is introduced as a computational technique to experimentally study molecular systems using molecular dynamics or Monte Carlo methods. Some key developments in the history of molecular simulations are also briefly outlined.
This document provides an overview of a course on molecular simulations. The course will cover topics like classical statistical mechanics, Monte Carlo and molecular dynamics simulations, modeling of molecules using different potentials, and techniques like free energy calculations and phase equilibrium simulations. Students will be expected to write simulation programs in languages like Fortran, C or C++. The course will be graded based on assignments, projects, mid-semester and end-semester exams. Molecular simulation is introduced as a computational technique to experimentally study molecular systems using molecular dynamics or Monte Carlo methods. Some key developments in the history of molecular simulations are also briefly outlined.
This document provides an overview of a course on molecular simulations. The course will cover topics like classical statistical mechanics, Monte Carlo and molecular dynamics simulations, modeling of molecules using different potentials, and techniques like free energy calculations and phase equilibrium simulations. Students will be expected to write simulation programs in languages like Fortran, C or C++. The course will be graded based on assignments, projects, mid-semester and end-semester exams. Molecular simulation is introduced as a computational technique to experimentally study molecular systems using molecular dynamics or Monte Carlo methods. Some key developments in the history of molecular simulations are also briefly outlined.
This document provides an overview of a course on molecular simulations. The course will cover topics like classical statistical mechanics, Monte Carlo and molecular dynamics simulations, modeling of molecules using different potentials, and techniques like free energy calculations and phase equilibrium simulations. Students will be expected to write simulation programs in languages like Fortran, C or C++. The course will be graded based on assignments, projects, mid-semester and end-semester exams. Molecular simulation is introduced as a computational technique to experimentally study molecular systems using molecular dynamics or Monte Carlo methods. Some key developments in the history of molecular simulations are also briefly outlined.
Course content What is Molecular Simulation Some examples and history of simulation
IIT KANPUR Course content 3
Sl. No Topic No. of Hours
1. Elementary classical statistical mechanics, ensembles and fluctuations, partition function, ergodicity, 3 molecular distribution functions 2 Scope of Molecular Simulation, elementary concepts of temperature, structure of a simulation program, 2 periodic boundaries, generating initial configuration and velocities, property measurement, ensemble averaging, error estimation 3 Monte Carlo integration, importance sampling, Markov chain, transition-probability matrix, limiting 8 distribution, detailed balance, Metropolis algorithm, Monte Carlo simulation, and extension to other ensembles, simple biasing methods 4 Equilibrium molecular dynamics simulations of continuous potentials, integration algorithms, extended 7 Lagrangians and simulations in other ensembles, time correlation function, evaluation of transport coefficients, hybrid molecular dynamics/Monte Carlo methods 5 Modeling of molecules, including hard potentials, soft potentials, multi-atomic models. Torsion, stretch and 3 bend potentials, electrostatics and polarizability, Ewald sum and reaction field methods for treating long-range electrostatic interactions. Truncating potentials, rigid vs. non-rigid molecules, orientation, rotation matrix, quaternion, Monte Carlo rotations 6 Free energy calculations: 5 Examination of several methods: thermodynamic integration, free-energy perturbation, parameter hopping, histogram methods. 7 Phase equilibria and interfacial properties 7 Introduction to various methods for calculating phase coexistence and interface properties: Gibbs ensemble MC, Gibbs-Duhem Integration, NVT + test particle, grand canonical MC. 8 Advanced techniques 5 Histogram reweighting method, transition-matrix MC, Wang-Landau sampling scheme, Rosenbluth sampling and configurational bias methods and parallel tempering.
IIT KANPUR Text books and Computer Usage 4
Text Books Statistical Mechanics, D. A. McQuarrie Understanding Molecular Simulation: From Algorithms to Applications, Frenkal and Smit Computer Simulation of Liquids, M.P. Allen and D.J. Tildesley Art of molecular dynamics by D. C. Rapaport Computer Usage This course will describe and discuss molecular simulation algorithms. Students are • expected to write their own program or modify the program given by the instructor. Fortran 90/C/C++ will be the standard language in the course. Computer Lab This course may have few labs to expose various academic and commercial s/w, such as DLPOLY, GROMACS LAMMPS IIT KANPUR 5
Course grading
Grading scheme Assignments and projects : 40% Mid Sem : 20% End Sem : 40%
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What is Molecular Simulation?
Molecular simulation is a computational “experiment” conducted on a 10 to 100,000 or more atoms are simulated molecular model (typically 500 - 1000)
Mica:
Cyclohexane:
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What is Molecular Simulation?
Phase Space
Many configurations are generated, and averages
taken to yield the “measurements.” One of two methods is used: Molecular dynamics Monte Carlo Integration of equations of motion Ensemble average Deterministic Stochastic Retains time element No element of time Molecular simulation has the character of both theory and experiment Applicable to molecules ranging in complexity from rare gases to polymers to metals IIT KANPUR What is a Molecular Model? 8
A molecular model postulates the interactions between
Separation More realistic models require other interatomic contributions • Intramolecular stretch, bend, out-of-plane bend, torsion, +intermolecular terms • Intermolecular van der Waals attraction and repulsion (Lennard-Jones form) electrostatic multibody IIT KANPUR 9
Why Molecular Simulation?
Molecular simulation is the only means for accurately
determining the thermophysical properties of a molecular model system model and treatment Theory Experiment
test treatment test model
Simulation
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Science explored by computational
Enrico Fermi’s Monte Carlo calculation of neutron
diffusion (1930’s) • 12 “hard sphere” atoms Hydrodynamics simulations required for the Manhattan Project (1940’s) Molecular dynamics simulations for materials science (1960’s) and later (1970’s) for protein structure Quantum Monte Carlo calculation of electron gas density (1980) - became the basis for density functional theory calculations https://en.wikipedia.org/wiki/Manhattan_Project IIT KANPUR 11
Molecular Simulation: a new science
1953(Metropolis et al) : First Monte Carlo simulation of a
molecular system
IIT KANPUR Molecular Simulation: a new science 12
1957 (Alder and Wainwright): First MD
• The purpose of the paper was to investigate the phase diagram of a hard sphere system, and in particular the solid and liquid regions. 1957 (Wood and Jacobson) : Recalculated EOS of HS leading to debate
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Molecular Simulation: a new science
The article Dynamics of radiation damage by J. B. Gibson,
A. N. Goland, M. Milgram and G. H. Vineyard from Brookhaven National Laboratory, appeared in 1960 , is probably the first example of a molecular dynamics calculation with a continuous potential based on a finite difference time integration method. The paper describes creation of defects induced by radiation damage, a theme appropriate to cold war days.
J. B. Gibson et al. Phys. Rev. 120, 1229 (1960).
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Molecular Simulation: a new science
Aneesur Rahman (1964):
First molecular dynamics with interatomic potential ( Ar-
Ar) • Aneesur Rahman also known as father of molecular dynamics
Rahman and Stillinger (1974): First MD with interatomic
potential (H2O-H2O) McCammon et al ( 1977): First MD of a protein
The American Physical Society annually awards the Aneesur Rahman Prize for outstanding achievement in computational research. First awarded in 1993, the Aneesur Rahman Prize is the highest honour in the field of computational physics given by the American Physical Society IIT KANPUR General Uses of Molecular Simulation 1. 15
Abstract models include only the most important
qualitative aspects • Examples Hard spheres Lattice models Point dipoles, quadrupoles Energy
Separation
• Lessons Attraction is needed to condense, but not to freeze Molecular diffusion is coupled to molecular convection No analytic equation of state can describe the critical region Volume fraction takes the role of mole fraction in describing macromolecular systems Quadrupole moments raise the triple point relative to the critical point In these applications, molecular simulation is a tool to guide theory IIT KANPUR 16
General Uses of Molecular Simulation 2.
Realistic models include the greatest feasible detail to give quantitative predictions and explanations • Features Lennard-Jones forms Multisite Point charges, polarizable Very specialized • Applications Biochemical systems (1 atm, 25ºC) Processes inside of zeolites Alkane critical properties with chain length Fits of individual properties (e.g., density, liquid enthalpy) to experiment for a few systems In these applications, molecular simulation has the potential to guide, and in some instances replace, experiment IIT KANPUR 17
Molecular simulation for engineers
Mechanical Thermophysical Stress-strain relationships Normal boiling point, Critical properties Elastic moduli Densities, Vapor pressure Glass temperature Viscosities, Diffusivities Poisson’s ratio Surface tension Tensile strength Mixture phase equilibria Yield stress Acentric factor, Solubility factor Viscoelasticity Molecular size and surface area Activity coefficient at infinite dilution Henry’s law constant Change in volume on mixing Change in enthalpy on mixing Change in Gibbs free energy on mixing VLE, PVT of mixtures Second and third virial coefficients Crystal habit Polymer void volume Adsorption isotherms Hydrophobicities
IIT KANPUR Molecular simulations in progress 18
MD usage
AICHE J, 55, 1304 (2009)
The field is still in its infancy: 40 years vs. > 400 years of experimental science
Molecular Electronics JCP, 124,144707 (2007) Nano-wire: Molecular Electronics Organic molecules between two electrode is a prototype of metal-molecule-metal configuration of molecular electronic
Molecular break-junction technique to test metallic electrode
Transition can be induced by vertical vibration1, pressure2, external force3.
1. Bormashenko et. al., Langmuir, 23 (2007)
DG = ò () f z z dz z0 2.Yang. et. al., J. Eur. Phys, 25 (2008) 3.Koishi et al. PNAS.106 (2009) IIT KANPUR 33
Cassie-Wenzel phase transition
Pure water drop 10 wt% ethanol
Metya et al. J. Phys. Chem. C 118, 4113 (2014)
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Commercial and academic s/w
Material Studio-Accelrys Quantum, Meso, MD, MC (limited) DLPOLY- MD, Meso Limited to 30,000 atoms GROMACS-MD Biological molecules NAMD-MD, AMBER, CHARMM LAMMPS CPMD TOWHEE-Monte Carlo Code Anu s/w- MC/MD/DEM s/w in progress at IIT Kanpur Etomica Educational and research tool in Java. MC, MD package Web: http://www.etomica.org http://rheneas.eng.buffalo.edu/wiki/Modules CACHE-Molecular Modeling Task Force http://www.et.byu.edu/~rowley/WebModules/modules.htm
