Hello, U can generate the restart files for last common frame in all your trajectory and use the same for continuing the simulation .
On Sat, Sep 4, 2010 at 3:16 PM, Berk Hess <[email protected]> wrote: > Hi, > > In gromacs 4.0 the checkpoint files of the different replicas might not be > in sync (written at the same step). > In that case you will have to use tpbconv with the trajectory of each > replica and select the last common frame. > > In the 4.5 release I fixed this issue by synchronizing the checkpointing. > > Berk > > ------------------------------ > From: [email protected] > > To: [email protected] > Date: Fri, 3 Sep 2010 09:31:38 +1000 > Subject: Re: [gmx-users] Restart Replica Exchange > > > ----- Original Message ----- > From: Nimesh Jain <[email protected]> > Date: Friday, September 3, 2010 1:13 > Subject: [gmx-users] Restart Replica Exchange > To: Discussion list for GROMACS users <[email protected]> > > > 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 > -- gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the > archive at http://www.gromacs.org/search before posting! Please don't post > (un)subscribe requests to the list. Use the www interface or send it to > [email protected]. Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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