Restarting an FEP simulation

From: Shyno Mathew (
Date: Wed Mar 05 2014 - 12:43:48 CST

Dear all,
We had to shutdown our cluster recently and this terminated all the FEP
runs. I haven't restarted an FEP before.
For each window, I have 10,000 equilibration steps followed by 20,000
production steps.My system was crashed for the lambda window 0.58 to
0.5825. From the .fepout file, it looks like only 850/10000 equilibration
steps were done.

Looking at the previous post, this is what I think I should do:
1. Run FEP for the window where it was crashed, here 0.58 to 0.5825
My restart frequency is 1000 fs. Since it crashed at 850, I assume I can do
the whole equilibration.
But I have other systems which crashed at 1050 fs, here I only do part of
the equilibration?

2. Then use the restart files to run the remaining FEP, 0.5825 to 1 and
manually combine the .fepout files.


Shyno Mathew
PhD student
Department of Chemical Engineering
Columbia University

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