[gmx-users] demux.pl input file

[Justin Lemkul]

On 9/2/15 8:48 AM, Nawel Mele wrote:
> 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??
>

Let's clear something up and make sure there is no misunderstanding.  When I say 
"multiple runs" I am not simply referring to the fact that there are multiple 
simulations going on in REMD.  That's obviously going on.  What I mean is this: 
demux.pl processes a .log file and tells you when exchanges happen.  So you need 
one .log file.  If you have split your procedure into multiple *intervals of 
time* you will have multiple runs per replica, in which case you need to 
concatenate the .log files *of one replica* to pass to demux.pl; if you did 
everything in one shot there is no need for anything fancy and you just run 
demux.pl on one .log file.

I hope this is clear.

-Justin

> 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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>
>

-- 
==================================================

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

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