[gmx-users] demux.pl input file

[Justin Lemkul]

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.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
>>> --
>>> Gromacs Users mailing list
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>>
>>
>>
>> --
>> Andrea Pérez Villa
>> *"Res non Verba"*
>> --
>> Gromacs Users mailing list
>>
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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.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================