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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
can learn about dynamical properties.
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
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
Time-correlation function
CAB ( ), CAA ( )
CAA ( ) =< A(0)A( ) >= limT
dtA(t)A(t + ) /T
Time-correlation function
caging
1
D=
3
caging
1
D=
3
caging
1
D=
3
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
d e
#
CAA ( )
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
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
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!)
Other techniques 2. CG
http://www.eng.buffalo.edu/~kofke/ce530/Lectures/Lecture12/sld001.htm
Other techniques 2. CG
net velocity over this time interval n3 t
http://www.eng.buffalo.edu/~kofke/ce530/Lectures/Lecture12/sld001.htm
Other techniques 2. CG
net velocity over this time interval n3 t
http://www.eng.buffalo.edu/~kofke/ce530/Lectures/Lecture12/sld001.htm
Other techniques 2. CG
net velocity over this time interval n3 t
http://www.eng.buffalo.edu/~kofke/ce530/Lectures/Lecture12/sld001.htm