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

[Berk Hess]

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
>>_______________________________________________
>>gmx-users mailing list    gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please don't post (un)subscribe requests to the list. Use the www 
>>interface or send it to gmx-users-request at gromacs.org.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>_______________________________________________
>gmx-users mailing list    gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the www interface 
>or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
Hotmail en Messenger on the move http://www.msn.nl/services