[gmx-users] Keeping replica numbers consistent when restartinga replica exch

[Robert Johnson]

Great! Thanks Berk. That seemed to work perfectly.
Bob

On 1/29/07, Berk Hess <gmx3 at hotmail.com> wrote:
> You can avoid this problem by catting the log files
> and then running the demux script on the concatenated log file.
>
> Berk.
>
>
> >From: Yang Ye <leafyoung81-group at yahoo.com>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] Keeping replica numbers consistent when
> >restartinga    replica exchange simulation
> >Date: Sat, 27 Jan 2007 05:55:45 +0800
> >
> >You may consider modify line 84 to 87
> >
> >         for($k=0; ($k<$nrepl); $k++) {
> >            $order[$k] = $k;
> >            $revorder[$k] = $k;
> >         }
> >
> >To read in the data in the last line of the previous replica_index.xvg and
> >replica_temp.xvg.
> >
> >Regards,
> >Yang Ye
> >
> >On 1/27/2007 5:05 AM, Robert Johnson wrote:
> >>Hello everyone,
> >>I'm currently running REMD and using the demux.pl script provided by
> >>David to generate replica_index.xvg and replica_temp.xvg files. I
> >>noticed that each time you restart the simulation (e.g. to extend the
> >>trajectory), all information about the replica index number is lost
> >>and the replicas are renumbered based on the index of their .tpr file.
> >>For example, I am restarting my runs every 1.2 ns. Say that after this
> >>time replica 0 contains the coordinates of replica 42. This will be
> >>evident in the run0_replica_index.xvg file for that particular run.
> >>However, this information is not passed to the subsequent .log files
> >>that provide information about the REMD swaps. Thus, the
> >>run1_replica_index.xvg file will show that replica 0 had the
> >>coordinates of replica 0 at the beginning of run1. Are there existing
> >>scripts that correct for this?
> >>Thanks,
> >>Bob Johnson
> >>_______________________________________________
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> >
> >
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