

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

 
