From: George Tzotzos <gtzotzos.me.com>
Date: Tue, 13 Mar 2012 18:06:14 +0100

I'm referring to Case et al., 2003 "Insights into Protein–Protein Binding by Binding Free Energy Calculation and Free Energy Decomposition for the Ras–Raf and Ras–RalGDS Complexes" and in particular the the part in which it is stated that "Previous studieshave shown that 100 – 200 snapshots are sufficient to estimate mean values with reasonable precision,62,63 since the error in the mean decreases with the square-root of the number of snapshots, provided that the sample points are independent."

My question is how does one ensure that the sample points are independent? I guess the independence of sample points is determined by the interval in the mmpbsa.in file. Am I right in this assumption? If yes, is there a rule of thumb in setting the interval value?

Thanks in advance

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Received on Tue Mar 13 2012 - 10:30:02 PDT
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