On 9/2/15 6:35 AM, Nawel Mele wrote:
Dear Andrea,
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
space.
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??
GROMACS trajectory and energy files are continuous in temperature, so you do not
need demux.pl to analyze a the properties at a particular temperature. If you
want to follow a particular structure through temperature space, you need
demux.pl. Any .log file should tell you about the exchanges; demux.pl simply
reads this information to write the appropriate output files to determine how to
follow a given structure through temperature space.
-Justin
Thanks again,
Nawel
2015-09-02 11:26 GMT+01:00 Andrea Pérez-Villa <a.pervi...@gmail.com>:
Dear Nawel,
You need to concatenate the log files of replica "0".
Regards,
Andrea
2015-09-02 12:16 GMT+02:00 Nawel Mele <nawel.m...@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
and
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
the
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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==================================================
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.
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