Dear Amber,
We have a question about calculating correlation time of mmP(G)BSA dG
values. After consulting the amberTools 13 manual, old mailing
list<
http://archive.ambermd.org/200712/0070.html>and the manuscripts
using the statistical inefficiency method (J. Chem.
Phys. 120, 2618 (2004); doi: 10.1063/1.1638996 & J Comput Chem 31:
837–846, 2010 ), we assume the following way is correct to calculate
correlation time of dG in mmP(G)BSA?
1. Run MD simulation and save the trajectory in every picosecond (ps).
2. Calculate mmP(G)BSA dGbind using every ps snapshot from the MD
trajectory. Save the .csv file during mmP(G)BSA (Activate -eo flag).
3. Write a script to calculate the dGbind correlation time using dGbind
of each snapshot from the .csv file by the statistical inefficiency method.
* statistical inefficiency method: correlation time= (block length) *
(the variance of the block average of X) / (the variance of the
distribution (X))
Any comment would be helpful. Thanks.
Cheers,
Henry
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Received on Tue Aug 27 2013 - 17:00:02 PDT
