[gmx-users] demux.pl input file

Justin Lemkul jalemkul at vt.edu
Wed Sep 2 14:38:27 CEST 2015

On 9/2/15 8:33 AM, Nawel Mele wrote:
> Dear Justin,
> Thank you for your answer,
> So from the REMD simulation we get different output files:
> - .trr : trajectory file
> - .edr : energy file
> - .cpt: checkpoint used in case of crash
> - .log
> I am not use to perform REMD with gromacs so I am not sure which files do I
> need to concatenated to obtain my xvg trajectory. I assume is .trr because
> it is the trajectory file, but because it is a binary file I am not sure.

You should spend some time reading the manual and doing some tutorials.

An .xvg is not a trajectory; it is a plain text data format.  If you have 
multiple intervals of time, you need to concatenate the .log files to process 
via demux.pl - to provide you the information you (might) need, you have to have 
information about the whole trajectory.

> If I well understand you I don't need to use demux.pl to extract for
> example angle of my simulation at a certain temperature but using


> replica_temp.xvg file from the demux.pl file to evaluate if the lowest
> temperature go through all temperature space is incorrect ??  Should I


> create my own script with the *_0.log file to follow the temperature
> trajectory through temperature space?

I don't know why you think you need your own script; this is exactly what 
demux.pl is for.

In any case, properly invoking demux.pl depends on how you did the run.  If you 
ran everything in one interval, just:

demux.pl md_0.log

If you ran in multiple intervals:

cat *_0.log > all.log (assuming you have md_0.log, md1_0.log, etc or some such 
perl demux.pl all.log



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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