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Hi,<br><br>In gromacs 4.0 the checkpoint files of the different replicas might not be in sync (written at the same step).<br>In that case you will have to use tpbconv with the trajectory of each replica and select the last common frame.<br><br>In the 4.5 release I fixed this issue by synchronizing the checkpointing.<br><br>Berk<br><br><hr id="stopSpelling">From: mark.abraham@anu.edu.au<br>To: gmx-users@gromacs.org<br>Date: Fri, 3 Sep 2010 09:31:38 +1000<br>Subject: Re: [gmx-users] Restart Replica Exchange<br><br>----- Original Message -----<br>From: Nimesh Jain <nimeshjain2010@u.northwestern.edu><br>Date: Friday, September 3, 2010 1:13<br>Subject: [gmx-users] Restart Replica Exchange<br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hi,<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>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?<br><br>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.<br><br>Mark
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