1

CE 530 Molecular Simulation

Lecture 1
David A. Kofke
Department of Chemical Engineering
SUNY Buffalo
kofke@eng.buffalo.edu

Multi-Scale Modeling
Continuum
Methods

Based on SDSC Blue Horizon (SP3)

1.728 Tflops peak performance
CPU time = 1 week / processor

Time/s
100

Atomistic
Simulation
Methods

(ms) 10-3

Mesoscale methods
Lattice Monte Carlo
Brownian Dynamics
Dissipative Particle Dynamics

(s) 10-6

(ns) 10-9

(ps) 10-12

Semi-empirical
methods
Ab initio
methods

Tight-binding
MNDO, INDO/S

(fs) 10-15

10-10

10-9

Monte Carlo (MC)

Molecular Dynamics (MD)

10-8

10-7

(nm)

10-6

10-5

10-4

(m)

Length/m
F.R. Hung, K.E. Gubbins, and S. Franzen, Chemical Engineering Education, Fall 2004

Electronic Scale: ab initio

Basic idea
Calculate properties from first principles by solving Schrdinger
equation numerically.

Pros

Cons

Can handle bond breaking/

formation processes
Can be improved
systematically, allowing
assessment of quality
Can in principle obtain exact
properties from input of only
atoms in system

Can handle only small systems,

on order 102 atoms
Can study only fast processes,
on order of 10 ps
Approximations necessary to
solve equations

Electronic Scale: semi-empirical

Basic idea
Use simplified versions of equations from ab initio methods (e.g.,
treat only valence electrons); include fitting parameters.

Pros

Cons

Can handle bond breaking/

formation processes
Can handle larger systems, of
order 103 atoms
Can be used for longer time
scales, on order of 10 ns

Difficult to assess the quality of

the result
Need experimental input and
large parameter sets
Parameters for one behavior
may not be best for another
(non-transferable)

Classical Atomistic Scale: Molecular Simulation

Basic idea
Use empirical or ab initio derived force fields, and sample atom
configurations to determine thermophysical properties.

Pros

Cons

Can handle larger systems, of

order 106 atoms
Can be used for longer time
scales, on order of 1 s
Can provide a broad range of
properties all consistent to
same molecular model

Tradeoff between quality of

model and size/time accessible
to simulation
Some behaviors occur on time
scales still inaccessible (e.g.,
diffusion in solids, many
chemical reactions, protein
folding, micellization)
Lose electronic properties, rxns

Meso-Scale Modeling
Basic idea
Average out faster degrees of freedom and/or treat large groups
of atoms as single entities with effective interactions.

Pros

Cons

Can handle larger systems, of

order 109 atoms
Can be used for longer time
scales, on order of seconds

Often provides only qualitative

information; difficult to assess
correctness of quantitative data
Approximations limit ability to
physically interpret results; key
information is lost or averaged
out

Continuum Modeling
Basic idea
Assume that matter is continuous and treat system properties as
fields. Numerically solve balance and constitutive equations.

Pros

Cons

Can handle systems of any

macroscopic size and time
scale
Input properties often
accessible from experiment

Requires specification of
constitutive model
Requires data from experiment
or lower-level method
Cannot explain molecular
origins of behavior

Multi-Scale Modeling
Continuum
Methods

Based on SDSC Blue Horizon (SP3)

1.728 Tflops peak performance
CPU time = 1 week / processor

Time/s
100

Atomistic
Simulation
Methods

(ms) 10-3

Mesoscale methods
Lattice Monte Carlo
Brownian Dynamics
Dissipative Particle Dynamics

(s) 10-6

(ns) 10-9

(ps) 10-12

Semi-empirical
methods
Ab initio
methods

Tight-binding
MNDO, INDO/S

(fs) 10-15

10-10

10-9

Monte Carlo (MC)

Molecular Dynamics (MD)

10-8

10-7

(nm)

10-6

10-5

10-4

(m)

Length/m
F.R. Hung, K.E. Gubbins, and S. Franzen, Chemical Engineering Education, Fall 2004

What is Molecular Simulation?

Molecular simulation is a computational
experiment conducted on a
molecular model.
10 to 100,000 or more
atoms are simulated

(typically 500 - 1000)

Many configurations are generated, and averages taken to yield the

measurements. One of two methods is used:
Molecular dynamics
Integration of equations of motion
Deterministic
Retains time element

Monte Carlo
Ensemble average
Stochastic
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?

A molecular model postulates the interactions between molecules
Energy

A typical two-body, spherical potential

(Lennard-Jones model)

1.5
1.0

12 6
u(r) = 4
r
r

0.5
0.0
-0 .5

-1 .0
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

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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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Example Use of Molecular Simulation 1.

Ideal gas equation-of-state
macroscopic model
P = RT

P = pressure (bar)
= molar density (moles/liter)
R = gas constant (0.08314 bar-liter/mol-K)
T = absolute temperature (K)

molecular model
U(r) = 0

no molecular interactions

macroscopic model can be derived exactly from molecular model

deviation of ideal gas EOS with experiment indicates failing of molecular model
no need for simulation
nevertheless, instructive to consider its application

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Example Use of Molecular Simulation 2.

Particles move at constant velocity until collision with wall
Pressure as a momentum flux
(px,py)
P=(momentum to wall)/area-time
F/A [=] (mL/t2)/L2 [=] (mL/t)/L2-t [=] p/A-t

elastic collisions with container walls

momentum transfer per collision

p = 2 p x

sum over collisions for unit of time

pressure is not given exactly, but as an average

1 t
P =
p

Ato t =0
o

(-px,py)

sum over long time to, or over many time origins, to get precise average

Click for Ideal-gas simulation

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Example Use of Molecular Simulation 3.

Interacting particles
hard spheres
particles move at constant velocity
until collision with another disk
or a wall
elastic collisions
cannot solve for exact EOS

Approximate EOS
Percus-Yevick
virial

1 + 2 + 3 2
Pv = kT
(1 ) 2
compressibility
1+ +2
Pc = kT
(1 )3

Cannot compare to experiment to resolve quality of these formulas

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General Uses of Molecular Simulation 1.

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

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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, 25C)
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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Water and Aqueous Solutions

GEMC simulation of water/methanol mixtures
Excellent agreement between simulation and experiment
1.0
0.8
0.6
y
0.4
Expt.
GEMC

0.2
0.0
0.0

0.2

0.4

0.6

0.8

1.0

Strauch and Cummings, Fluid Phase Equilibria, 86 (1993) 147-172; Chialvo and
Cummings, Molecular Simulation, 11 (1993) 163-175.

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Phase Behavior of Alkanes

Panagiotopoulos group
Histogram reweighting with finite-size scaling

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Alkane Mixtures
(Supercritical) Ethane + n-Heptane

Siepmann group
Ethane + n-heptane

10
Exp. at 366 K
TraPPE-EH at 366 K
Exp. at 450 K
TraPPE-EH at 450 K

P [MPa]

8
6
4
2
0
0

0.2

0.4

0.6
Xethane

0.8

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Kinematic Viscosity Index of Squalane

squalane (C30H62)

Calc. 311K

100

Calc. 372 K
Expt. (Newtonian) viscosity

Predicted: 10318

Pred. transition to shear-thinning

(10-6 m2/s)

Viscosity

Experiment:
11630

10

0.1
Moore, 0.0001
J. D., Cui, S. T., Cummings,
P.
0.001

0.01 Shear rate

0.1
T. and Cochran, H. D., AIChE Journal, (1012 s-1)
43 (1997) 3260-3263

Figure 1: Moore, Cui, Cummings and Cochran

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(Image of alkanes)