[gmx-users] demux.pl input file

[Nawel Mele]

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.

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?

Thank you very much,

Nawel


2015-09-02 13:15 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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
>>>>
>>>> * Please search the archive at
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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
>
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-- 

Nawel Mele, PhD Research Student

Jonathan Essex Group, School of Chemistry

University of Southampton,  Highfield

Southampton, SO17 1BJ