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Module-3: Ab Initio Molecular Dynamics

This document discusses how molecular dynamics (MD) simulations are useful for computing time-dependent properties, transport properties, and structural properties from a molecular system. It provides examples of using MD simulations to calculate correlation functions to obtain vibrational spectra, diffusion constants using the Green-Kubo and Einstein relations, equilibrium configurations, and distribution functions like the radial distribution function g(r) to understand molecular structure and interactions. MD simulations are limited by timescale and can typically access phenomena on the picosecond timescale and above depending on the system and energy barriers involved in the process of interest.

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Anubhav Vardhan
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49 views18 pages

Module-3: Ab Initio Molecular Dynamics

This document discusses how molecular dynamics (MD) simulations are useful for computing time-dependent properties, transport properties, and structural properties from a molecular system. It provides examples of using MD simulations to calculate correlation functions to obtain vibrational spectra, diffusion constants using the Green-Kubo and Einstein relations, equilibrium configurations, and distribution functions like the radial distribution function g(r) to understand molecular structure and interactions. MD simulations are limited by timescale and can typically access phenomena on the picosecond timescale and above depending on the system and energy barriers involved in the process of interest.

Uploaded by

Anubhav Vardhan
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Module-3

Ab Initio Molecular
Dynamics
April 08

How MD Simulations are


Useful?

Computing Time Dependent Properties


as MD generates conformation as a
function of time
Correlation Functions: Cxy

M
X
1
=
xi yi hxi yi i
M i

Normalised correlation function:


PM
1
hxi yi i
i x i yi
M
P
2
cxy = P
2i
M 2
M 2
1
1
hx
i
hy
i
i
x
y
i
i
i
i
M
M
(this varies between -1 and +1)

time correlation functions


Cxy (t) = hx(t)y(0)i

This is called as cross correlation function if x and y


are different quantities and auto correlation function if x
and y are the same quantities

velocity auto correlation:


N D
E
X
1
Cvv (t) =
R I (t) R I (0)
N
0
I

Normalized velocity auto correlation function

1
cvv (t) =
N

N
X
I

R I (t) R I (0)

R I (0) R I (0)

E0

average
over
time
origins

highly correlated:

d exp( 2i )cvv ( )

intensity, I

I() =

2840

2880

freq. (cm-1)

less correlated (short memory!)

vibrational spectrum can thus


be obtained

dipole moment time correlation


data can be used for simulating
IR spectrum

Transport Properties
Self Diffusion constant:
D
E
P
N
2
1
|RI (t) RI (0)|
I
N
3 D = lim
t!1
2t
=

1
0

N D
E
X
1
I (t) R
I (0)
dt
R
N
I

Einstein

GreenKubo

Computing Structural Properties

Constant temperature
MD take a molecular
system to equilibrium
configurations (with
highest Boltzman
weight, exp( H))

PE
R

PE
t

P
R

PE
PE

rxn coordinate

Depends on the Boltzman weight near TS!

trxn?

Timescale

AB

B A
F

F
A

kB T
1/ = k
exp
AB
AB
h

FAB
kB T

at T=300K
Barrier (kJ/mol)

Timescale

MD steps (1fs
timestep)

2.5

0.1 ps

100

10

1 ps

1000

20

0.1 ns

106

60

1 ms

1012

100

8 hrs

1020

0.4

0.5

2.4 (0.5)

1.4

VOL 330

Reaction coordinate (s)

lding kinetics
0.8 A
B
energy barrier.
gy profile along
state
0.6
reaction coorprofile exhibits
centered at 0.1
0.4
sponding to the
nfolded basins,
0.2
he folding and
ee-energy barstate
T and 3.5kBT,
0
B) Langevin sim0
1
2
3
0
20
40
60
80
100
W folding in a
Free energy (kBT)
Time (s)
nal model. The
as based on the one-dimensional free-energy profile in (A) and a position-dependent
fficient, both derived from the MD simulation data.

F
(s)
=
k
T
ln
P
(s)
B
SCIENCE www.sciencemag.org
normalized
histogram of s(t)

Distribution functions can thus give an idea


of most probable values of the coordinates
(and thus the structure)

P(s)
1
P (s ) =
Q

Q=

Z=

d R exp

1
) P (s ) =
Z
0

h (s

U (R )

d R exp
0

s )i

d R d P exp

d R d P exp

s
N

U (R )

H(R , P )

H(R , P )

(s(RN )

s0 )

(s(RN )

s0 )

Radial Distribution Function g(r)


Pair-Correlation function or distribution
function (for spatial correlation in
structural motions)

Many body

interactions
equilibrium structure is
complicated to
understand looking at
the snapshots

(N 1)
h
(r
Definition: g(r) =
4r2

normalization
g(r) = 1
r0 )i for ideal density

count number of atoms


within the thin shell
at a given distance r and
average over atoms and
frames
r

Radial Distribution
Function g(r)
density 4 times
higher than uniform
density

density close to the


uniform density
long-range order

D. Chandler
Stat. Mech.

Importance of g(r)
(contd.)
g(r) is related to

structure factor (Fourier


transform)

thermodynamic properties

Real gases: e.g. constant a in


VdW EOS

Bhargava, Balasubramanian and Klein,


Chem Comm. 2008

Simulation of soft condensed


matter systems
Solvent effect & finite temperature effect

potential energyfree energy

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