[gmx-users] demux.pl input file

[Nawel Mele]

2015-09-02 13:38 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 9/2/15 8:33 AM, Nawel Mele wrote:
>
>> 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.
>>
>>
> You should spend some time reading the manual and doing some tutorials.
>
> An .xvg is not a trajectory; it is a plain text data format.  If you have
> multiple intervals of time, you need to concatenate the .log files to
> process via demux.pl - to provide you the information you (might) need,
> you have to have information about the whole trajectory.
>



> 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
>>
>
> Correct.
>
> replica_temp.xvg file from the demux.pl file to evaluate if the lowest
>> temperature go through all temperature space is incorrect ??  Should I
>>
>
> Correct.
>
> create my own script with the *_0.log file to follow the temperature
>> trajectory through temperature space?
>>
>>
> I don't know why you think you need your own script; this is exactly what
> demux.pl is for.
>
> In any case, properly invoking demux.pl depends on how you did the run.
> If you ran everything in one interval, just:
>
> demux.pl md_0.log
>
> If you ran in multiple intervals:
>
> cat *_0.log > all.log (assuming you have md_0.log, md1_0.log, etc or some
> such convention)
> perl demux.pl all.log
>


I am use to perform simulation and specially REMD simulation with Amber
software. But in Amber, exchanges in temperature space are accomplished by
swapping temperature so a post processing is required to extract
temperature trajectory. That's why I am a bit confused with Gromacs REMD. I
know It must seems that I make you repeat but just to be sure, because I
have multiple run I need to concatenate my .log files and then use this
file into demux.pl to obtain information about the whole trajectory?? And
from that I can do any kind of analysis I want??

Many thanks


>
> -Justin
>
>
> --
> ==================================================
>
> 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