[gmx-users] Restart Replica Exchange
genomejani at gmail.com
Sat Sep 4 15:06:06 CEST 2010
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 <gmx3 at hotmail.com> wrote:
> 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.
> From: mark.abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Date: Fri, 3 Sep 2010 09:31:38 +1000
> Subject: Re: [gmx-users] Restart Replica Exchange
> ----- 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.
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