[gmx-users] Restart Replica Exchange

[Mark Abraham]

----- Original Message -----
From: Nimesh Jain <nimeshjain2010 at u.northwestern.edu>
Date: Friday, September 3, 2010 1:13
Subject: [gmx-users] Restart Replica Exchange
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Hi,
> 
> I was wondering if anyone knows whether it is possible to restart a replica exchange simulation if it stops during the run. I tried it once before and got the error that all the replicas should be at the same time step for replica exchange. When I checked the time step of different replicas, there was a few 10s of picoseconds difference b/w them. Is there a way to circumvent this problem and restart replica exchange?

This issue will normally only arise if your run finished abnormally. I seem to recall discussion of it somewhere. Perhaps you need to restart in a different manner (hint: telling us your command lines would have been useful), e.g. using the checkpoint files properly. Alternatively, since the differences cannot span a replica exchange, you could try running the lagging simulations in serial until they're all in sync.

Mark

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