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

Robert Johnson bobjohnson1981 at gmail.com
Fri Jan 26 22:05:03 CET 2007

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?
Bob Johnson

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