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# L9.

Molecular Dynamics VI
- Time correlation functions
Qiang Cui
Chem. 860
Spring 2009

Equilibrium? Dynamics?
Onsagers regression hypothesis: spontaneous
fluctuations in equilibrium regress back to
equilibrium according to the same relaxation
equation that describes the macroscopic
relaxation (due to external perturbation) provided that the perturbation is weak
By observing equilibrium fluctuations, one

Time-correlation function
CAB ( ), CAA ( )
CAA ( ) =< A(0)A( ) >= limT

dtA(t)A(t + ) /T

Time-correlation function
CAB ( ), CAA ( )
CAA ( ) =< A(0)A( ) >= limT

dtA(t)A(t + ) /T

## Short-time limit CAA (0) =< A(0)A(0) >=< A >

2

Time-correlation function
CAB ( ), CAA ( )
CAA ( ) =< A(0)A( ) >= limT

dtA(t)A(t + ) /T

2

## Long-time limit CAA () =< A(0)A() >=< A >

Time-correlation function
CAB ( ), CAA ( )
CAA ( ) =< A(0)A( ) >= limT

dtA(t)A(t + ) /T

2

## Shift to zero at long-time

!
( ) =< A(0)A( ) >=< (A(0) < A >)(A( ) < A >) >= CAA ( ) < A >2
CAA

Time-correlation function
CAB ( ), CAA ( )
CAA ( ) =< A(0)A( ) >= limT

dtA(t)A(t + ) /T

2

## Shift to zero at long-time

!
( ) =< A(0)A( ) >=< (A(0) < A >)(A( ) < A >) >= CAA ( ) < A >2
CAA

## Sometimes normalize as well

!
!
(0)
( )/CAA
CAA ( ) = CAA

Time-correlation function

caging

1
D=
3

caging

1
D=
3

caging

1
D=
3

## < v(0) v(t) > dt

2
C(0)
=<
v(0)

v(0)
>=<
v
>= dkB T /m
What is t=0 value?

More definitions
Correlation time
!

c =

"
( )/ < A2 >
d CAA

If

!
CAA ( )

/rel

then c = rel

1
IA () =
2

d e

#
CAA ( )

1
D=
3

## < v(0) v(t) > dt

R.G. Gordon, Correlation Functions for Molecular Motion, Adv. Mag. Resonance 3 (1968) 1
R. Zwanzig, Time-Correlation Functions and Transport Coefficients in Statistical Mechanics , Ann. Rev. Phys. Chem. 16 (1965) 67

Calculations of TCF
N
!
1
CAA ( ) =
Ai Ai+n
N i=1

= nt

Calculations of TCF
N
!
1
CAA ( ) =
Ai Ai+n
N i=1

http://www.eng.buffalo.edu/~kofke/ce530/Lectures/Lecture12/sld001.htm

= nt

During the MD

http://www.cbe.buffalo.edu/courses/ce530/Lectures/Lecture12/sld013.htm

During the MD
Cost: ~ n2

http://www.cbe.buffalo.edu/courses/ce530/Lectures/Lecture12/sld013.htm

During the MD
Cost: ~ n2

http://www.cbe.buffalo.edu/courses/ce530/Lectures/Lecture12/sld013.htm

c
< CAA ( ) >< A >
0
2

During the MD
Cost: ~ n2

http://www.cbe.buffalo.edu/courses/ce530/Lectures/Lecture12/sld013.htm

c
< CAA ( ) >< A >
0
2

## So the statistical error of TCF is independent of

thus the relative error for TCF increasely quickly
as increases
which makes the time integral of TCF difficult to
calculate accurately

TCF in CHARMM
coor anal - useful for analyzing solvent
properties (e.g., diffusion in homework!)
CORREL - a more general purpose facility to
calculate different kinds of TCF

## Other techniques I. FFT

http://en.wikipedia.org/wiki/Fast_Fourier_transform
http://mathworld.wolfram.com/FastFourierTransform.html
http://www.nr.com/

Other techniques 2. CG
Long-time behavior of TCF is expensive to
evaluate using the conventional technique
(has to store many info!)

## Long-time behavior doesnt depend on the

details of short-time behavior - so can
coarse-grain (CG) short-time data to
extract long-time behavior

Other techniques 2. CG

## (we have k levels)

http://www.eng.buffalo.edu/~kofke/ce530/Lectures/Lecture12/sld001.htm

Other techniques 2. CG
net velocity over this time interval n3 t

## (we have k levels)

http://www.eng.buffalo.edu/~kofke/ce530/Lectures/Lecture12/sld001.htm

Other techniques 2. CG
net velocity over this time interval n3 t

## (we have k levels)

http://www.eng.buffalo.edu/~kofke/ce530/Lectures/Lecture12/sld001.htm

Other techniques 2. CG
net velocity over this time interval n3 t

## (we have k levels)

http://www.eng.buffalo.edu/~kofke/ce530/Lectures/Lecture12/sld001.htm