Hello,<br>U can generate the restart files for last common frame in all your trajectory and use the same for continuing the simulation . <br><br><div class="gmail_quote">On Sat, Sep 4, 2010 at 3:16 PM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span> wrote:<br>
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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>From: <a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a><div class="im"><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
</div>Date: Fri, 3 Sep 2010 09:31:38 +1000<br>Subject: Re: [gmx-users] Restart Replica Exchange<div><div></div><div class="h5"><br><br>----- Original Message -----<br>From: Nimesh Jain <<a href="mailto:nimeshjain2010@u.northwestern.edu" target="_blank">nimeshjain2010@u.northwestern.edu</a>><br>
Date: Friday, September 3, 2010 1:13<br>Subject: [gmx-users] Restart Replica Exchange<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><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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