[gmx-users] demux.pl input file
nawel.mele at gmail.com
Wed Sep 2 12:35:23 CEST 2015
Thank you very much for your quick answer.
I would like to ask you another quick question. Like I said I am interested
on a particular temperature , so I wanted to use the demux.pl file to
follow the trajectory of my temperature of interest through the temperature
But, if I want the trajectory of this specific temperature in order to
perform different analysis on it like dihedral and hydrogen bond analysis.
Should I use first demux.pl on the replica "0" (for the lowest temperature)
and then use the replica_index.xvg output file and perform : trjcat -f
*.trr -demux replica_index.xvg or because during gromacs REMD simulation
only coordinates are exchanges do I need to use the demux.pl script for
extracting my trajectory??
2015-09-02 11:26 GMT+01:00 Andrea Pérez-Villa <a.pervilla at gmail.com>:
> Dear Nawel,
> You need to concatenate the log files of replica "0".
> 2015-09-02 12:16 GMT+02:00 Nawel Mele <nawel.mele at gmail.com>:
> > Dear Users,
> > I have performed a REMD simulation on a protein with 48 replicas. I have
> > 400ns of REMD simulation and by consequence several restart simulation
> > so several .log files:
> > run1_0.log , run1_0.log .... run1_47.log
> > run2_0.log , run2_0.log .... run2_47.log
> > .
> > .
> > .
> > runx_0.log , runx_0.log .... runx_47.log
> > I am interested on the lowest temperature trajectory and I want to use
> > demux.pl scriot.
> > I have been through many similar questions in the forum but I am still
> > confused how to use the demux.pl script.
> > Should I need to concatenate all my log files like this:
> > cat run1_1.log run2_1.log ... runx_1.log > run_total.log
> > cat run1_0.log run1_1.log run1_2.log ... run1_47.log
> > run2_0.log run2_1.log run2_2.log ... run2_47.log ...
> > runx_0.log runx_1.log runx_2.log ...runx_47.log > run_total.log
> > Many thanks for your help.
> > Nawel
> > --
> > Nawel Mele, PhD Research Student
> > Jonathan Essex Group, School of Chemistry
> > University of Southampton, Highfield
> > Southampton, SO17 1BJ
> > --
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> Andrea Pérez Villa
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Nawel Mele, PhD Research Student
Jonathan Essex Group, School of Chemistry
University of Southampton, Highfield
Southampton, SO17 1BJ
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