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ChE 622 Introduction to Molecular

Simulations

Lecture 1

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Overview

 Course content
 What is Molecular Simulation
 Some examples and history of simulation

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 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.

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 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
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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
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 What is a Molecular Model? 8

 A molecular model postulates the interactions between

molecules

1.5
Energy
1.0

0.5
 12  6 
u(r )  4  
0.0 
 r   r  

-0.5
A typical two-body, spherical potential
-1.0
(Lennard-Jones model)
1.0 1.2 1.4 1.6 1.8 2.0

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
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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
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Molecular Simulation: a new science

1953(Metropolis et al) : First Monte Carlo simulation of a

molecular system

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 Molecular Simulation: a new science
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 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
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 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
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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
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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

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 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

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Molecular Simulation: Engineering Tool

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Molecular Simulation: Engineering Tool

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Phase Behavior of Alkanes

 Errington and Panagiotopoulos

• Histogram reweighting with finite-size scaling

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Heat of adsorption

Wei Shi and Karl Johnson, PRL, 91, 015504, 2003

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Alkane Mixtures
(Supercritical) Ethane + n-Heptane

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 Siepmann group Exp. at 366 K
TraPPE-EH at 366 K
• Ethane + n-heptane Exp. at 450 K
8 TraPPE-EH at 450 K

6
P [MPa]

0
0 0.2 0.4 0.6 0.8 1
Xethane

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Wettability

SAM allows tailored

functional surface
• Corrosion barrier
• Anti fouling coatings
• Molecular electronics

Water on n- alkanethiolate
monolayer on gold

Langmuir, 21,12171 (2005)

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Lubrication at nanoscale
JCP, 125,104701
(2006)

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Bio-materials

Langmuir 2006, 22, 4116-4124

Thiolate molecules

Au (111) surface

Molecular
electronics

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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

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Virus modeling

Tobacco Mosaic Virus

http://www.ks.uiuc.edu/Gallery/Mo
vies/Virus/embed1.html
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Hepatitis B Virus – mechanical test

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Dynamics of water droplet on hydrated brush

layer

T = 280 K T = 320 K

30
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Contact Angle
• Increase in contact angle
beyond the LCST (305 K) of
bulk PNIPAAm

• Experimental data : 55-

65º to 78-88º

Bhandary et al , Soft Matter, 12, 3093 2016

31
Balamurugan et. al., Langmuir, 2003 Takei et. al., Macromolecules, 1994
Angew. Chem. Int. Ed. 2004, 43, 357 –360 IIT KANPUR
Cassie -Wenzel coexistence/transition 32

 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
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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

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