Questions about lambda scheme in free energy perturbation

From: Jian Dai (
Date: Tue Feb 24 2015 - 08:59:57 CST

Dear all:
I have questions about simulation scheme in FEP.
First, for example, if I divided the simulation into 10 windows for lambda
from 0 to 1, so that they are 0 - 0.1 (window 0), 0.1 - 0.2 (window 1), ...
0.9 - 1.0 (window 9), should I use the final coordinates of window 0 to
conduct simulation on window 1, and so on? Or in principle I could use the
same starting coordinates for all 10 windows? I guess it should be the
former scheme.
Second, if I later decide to add some intermediate windows, for example, I
want to add a window corresponding to lambda 0.05 - 0.1, is this
feasible?Or should I plan how the lambda should change before I start
Thank you in advance.

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