AMBER Archive (2006)

Subject: AMBER: How the ensemble average calculated in Gibbs, AMBER7?

From: Yongmei Pan (ypan2_at_uky.edu)
Date: Wed Nov 01 2006 - 16:06:09 CST

Hi, all

Just one question about how the ensemble average is calculated in the following equation:

G(i+1)-G(i)=-RTln<exp-[(V(i+1)-Vi)/RT]>i

for the samplings in states i and i+1, how the potential energie V(i+1) subtracted by Vi? Because we can not say, for example, the No.100 sampling from state i+1 corresponds to the No. 100 sampling from state i, how can we calculate the ensemble average of V(i+1)-Vi? Is the ensemble average calculated in such way that eachone of V(i+1) from one sampling of state i+1 is subtracted by all the V(i)s of every sampling from state i, and then the ensemble average is calculated by averaging the summation with n*n, n is the sampling number.

I hope the question is clear. I just ask this question to prepare for my qualify examination. Thanks!

Yongmei Pan

Yongmei pan
College of pharmacy, University of Kentucky

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu