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

From: Yongmei Pan <ypan2.uky.edu>
Date: Wed, 01 Nov 2006 17:06:09 -0500

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

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Received on Sun Nov 05 2006 - 06:07:16 PST
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