Dear Amber users,
I am trying to do dynamic cross-correlation analysis using ptraj on the
last 10 ns frames of my 50 ns long simulation of a globular protein.
Recently, I have gone through an article by van Gunsteren et al. (
http://www.sciencedirect.com/science/article/pii/S0022283685705141), where
the authors talking about the effect of averaging time on the dynamic
cross-correlation analysis and highlighted the changes in
cross-correlation maps plotted over different time window (set of 200ps
frames) on a 2ns long simulation. On a similar line, I have also carried
out correlation analysis ( for alpha carbon atoms) using different time
window and can able to see notable difference in the correlation map. Now I
am confused that, out all the different maps, which one will tell me about
the exact dynamics in the protein. Can anyone suggest me, which time
averaging can provide better picture of dynamic regions in protein?
Below provided the few scripts I used for the correlation calculation in
ptraj.
***********************************************
trajin md10.crd 1 2500
trajin md11.crd 1 2500
center :1-293 mass origin
image origin center
rms first mass :1-293
matrix correl :1-293.CA out corr.dat
**************************************************
rajin md10.crd 1 2500 5
trajin md11.crd 1 2500 5
center :1-293 mass origin
image origin center
rms first mass :1-293
matrix correl :1-293.CA out corr.dat
***************************************************
rajin md10.crd 1 2500 10
trajin md11.crd 1 2500 10
center :1-293 mass origin
image origin center
rms first mass :1-293
matrix correl :1-293.CA out corr.dat
**************************************************
rajin md10.crd 1 2500 50
trajin md11.crd 1 2500 50
center :1-293 mass origin
image origin center
rms first mass :1-293
matrix correl :1-293.CA out corr.dat
***************************************************
Waiting for your valuable suggestions.
Thanks in advance
Best regards
Aneesh
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Received on Sat Feb 02 2013 - 02:30:02 PST
