[gmx-users] demux.pl input file

[Justin Lemkul]

On 9/2/15 9:21 AM, Nawel Mele wrote:
> 2015-09-02 14:09 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> 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
>
>
> Thank you very much.
>
> It is all clear. I have multiple "run" per replica because I can't
> performed my simulation in one shot. From that I will concatenate all the
> run for the replica I am interesting on and use this "concatenate log file
> " as input for demux.pl .
> The point I am not totally clear is , in order to produce a trajectory of
> all the "run" for one replica can I just do :
>
> trjcat -f *0_.trr -o R0_all.trr
>

Yes.

> In this point, if I don't need continuous trajectory I don't need to
> specify -demux replica_index.xvg option in the trjcat command?
>

Just be careful with the language.  The trajectories *are* already continuous 
with respect to ensemble.  If you want them continuous with respect to 
structures, then you need -demux.

-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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