[gmx-users] demux.pl input file

[Nawel Mele]

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??

Thanks again,

Nawel


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".
> Regards,
>
> Andrea
>
> 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
> 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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>
>
> --
> Andrea Pérez Villa
> *"Res non Verba"*
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-- 

Nawel Mele, PhD Research Student

Jonathan Essex Group, School of Chemistry

University of Southampton,  Highfield

Southampton, SO17 1BJ