Molecular Dynamics

Basic Idea
Solve Newtons equations of motion
mj

d 2rj
dt

Fj ,

V
Fj
,
rj

j 1,2,L , N

Choose a force field (specified by a potential V)

appropriate for the given system under study
Decide a statistical ensemble to use, choice of
boundary conditions; collect statistics of
observables

Commonly Use Force Fields

Lennard-Jones Potential
For noble gas and generic fluids

Tersoff, Brenner, Stillinger-Weber, 3-, 4body potentials

For C, Si, Ge,

AMBER, CHARMM, GROMOS, MM4, etc

For biomolecules

GULP, DFT codes, etc

Example of potential used in

biomolecular modeling
2
2
ki
k i
V (r1,r2 ,L ,rN ) li li ,0
i i ,0

bonds 2
angles 2

Vn

1 cos(n )
torsions 2

12

q
q
ij
i j
4 ij ij
r
4 0rij
rij
i j
ij

Ensembles
Micro-canonical Ensemble
Energy is fixed

Canonical ensemble
Need to use thermostat to fix temperature
Langevin dynamics
Nos-Hoover
Generalized Langevin

Langevin Dynamics
d 2rj
2

Fj

dt
m
(t ) 0,
T

I
(t ) (t ')

vj ,

j 1,2,L , N

2 k BT

(t t ')
m

How to correctly implement the white noise

on computer?

Nos-Hoover Dynamics
r&j v j

pj

m
p&j Fj p j ,
1 K
1
2
&
2
1 , K mv j
K0
j 2

Generalized Langevin
& F
u&

(t t ')u(t ')dt '

(t ) 0,
(t ) (t ') i h(t t ')

is known as self-energy

Observables, Statistics
Equilibrium temperature (in micro-canonical
ensemble) by equipartition theorem.
1
1
k BT
m j v 2j , , x, y , z
2
2

Pressure of a fluid (for pair potential)

1
PV Nk BT
d

(r r ) F
i j

ij

Where d is dimension, Fij is the force acting on particle i

from particle j.

Transport Coefficients
The diffusion constant can be computed
through velocity correlation function

v(t ) v(0) dt lim

t

r (t ) r (0)
2t

3D

Transport Coefficients
Thermal conductivity can be computed
through energy-current correlation using
Green-Kubo formula; or nonequilibrium
simulation by directly computing the
energy current

Textbooks on MD
M P Allen & D J Tildesley, Computer
Simulation of Liquids, (Oxford, 1987)
D Frenkel & B Smit, Understanding
Molecular Simulation, 2nd ed (Academic
Press, 2002)
A R Leach, Molecular Modeling,
principles and applications (Addison
Wesley Longman, 1996)

Tutorial Problem Set 12

Prove the pressure formula (required a
great deal of knowledge of statistical
mechanics).