[gmx-users] Keeping replica numbers consistent when restarting a replica exchange simulation

Yang Ye leafyoung81-group at yahoo.com
Fri Jan 26 22:55:45 CET 2007

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.

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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