Window for FEP calculations

From: Gianluca Interlandi (
Date: Tue Aug 26 2014 - 19:35:33 CDT

Dear NAMD users,

I want to perform a FEP calculation where I mutate a residue in a protein
from methionine to methionine sulfoxide and calculate the DeltaG of the
transformation. Are there any guidelines about what an optimal window
length might be? I was planning to do the transformation during 10 ns. Is
it appropriate to use for example 100 windows (each window 100 ps) or is
it better to have less windows but longer?

The Ala-Tyr-Ala example in the FEP tutorial uses 20 windows of 0.5 ps
each. That is just an example of course.



Gianluca Interlandi, PhD
                     +1 (206) 685 4435

Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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