[gmx-users] Hope this can help someone using REMD in Gromacs

jia jia jzg579 at gmail.com
Mon Feb 2 18:43:03 CET 2015

Dear Gromacs User:
I found when after running REMD in gromacs and try to generate trajectories
for each replic based on the origin trajectories based on conditions, if
the exchange step is mower than 1ps, after time pint 100ns there will be
some noise "spikes" in the RMSD or other characters calculated from
trajectories for each replic.
The noise seems because when using "demux.pl", the output formart for time
is -20%g so you will get things like
399988   0
399988   1
399988   0
in your replica_index.xvg.
If you want to remove the noise, you can
1) add a line
"$timestep = XXX;" in beginning (XX is timestep with unit ps)
2) change print formart in line 33 and 44 from %-20g to %-20f
3) change the line 70 to $tstep = $log_time[4] * $timestep;

Note the results based on origin "demux.pl" is CORRECT, it just a little
Hope this can help someone using REMD.
Cheers: )
ZhiGuang Jia

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