Department of Chemical Engineering, IIT Kanpur

Introduction to Molecular Simulations

MWF: 9.00-9.50 am, FB 470
Instructor: Jayant K. Singh
NL II 202
Email: jayantks@iitk.ac.in
Phone: 2596141
Course Description
Molecular simulations of liquids, gases, metals, polymers, biological systems and other
complex fluids combined with contemporary experiments promise to revolutionalize our
ability to understand molecular world. This course aims to provide student with an
understanding of the methods, capabilities, and limitations of molecular simulation. This
should enable the student to make sound judgments regarding the quality of molecular
simulation studies reported in the literature and decide whether molecular simulation is
suited for application to their research, and if so, to know how to begin developing a
simulation program applicable to their problems. Further, it is expected that completion
of this course will leave the student with a much deeper understanding of the molecular
basis of physical behavior. The course will cover the following topics:
Detailed Course Content:
Statistical Mechanics (around 10 lectures)
Elementary classical statistical mechanics, ensembles and fluctuations, partition function,
ergodicity, ideal gas, non-interacting lattice models, adsorption isotherms, multilayer
adsorption, rubber elasticity, modeling of intermolecular potential, molecular distribution
functions
Molecular Simulation: Basic MC and MD: (15 lectures)
Scope of Molecular Simulation, elementary concepts of temperature, structure of a
simulation program, periodic boundaries, generating initial configuration and velocities,
property measurement, ensemble averaging, error estimation
Monte Carlo integration, importance sampling, Markov chain, transition-probability
matrix, limiting distribution, detailed balance, Metropolis algorithm, Monte Carlo
simulation, and extension to other ensembles, simple biasing methods
Equilibrium molecular dynamics simulations of continuous potentials, integration
algorithms, extended Lagrangians and simulations in other ensembles, time correlation
function, evaluation of transport coefficients, hybrid molecular dynamics/Monte Carlo
methods
Beyond atoms: Simulating molecules (3 lectures)

Modeling of molecules, including hard potentials, soft potentials, multiatomic models.

Torsion, stretch and 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
Free energy calculations, phase equilibria and interfacial propertries(10 lectures)
Examination of several methods: thermodynamic integration, free-energy perturbation
(including umbrella sampling), parameter hopping, histogram methods
Introduction to various methods for calculating phase coexistence and interface
properties: Gibbs ensemble MC, Gibbs Duhem Integration, NVT + test particle, grand
canonical MC
Advanced techniques (2 lectures)
Histogram reweighting method, transition-matrix MC, Wang-Landau sampling scheme,
complex fluids and biased-sampling techniques, Rosenbluth sampling and
configurational bias methods, parallel tempering
Efficiencies and parallel methods (1 lecture)
Look up tables, Verlet list, cell list, domain decomposition, replicated data, limitations on
parallel algorithms, Esselink method, and parallel replica method
Text book
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
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++will be the standard language in the course.
Computer Lab
This course will have few labs to expose various academic and commercial s/w
Grading scheme
1 Mid Sem
: 20%
1 End Sem
: 40%
Assignments and small projects: 40%