[gmx-users] demux.pl input file

Thu Sep 3 10:33:37 CEST 2015

2015-09-02 21:38 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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.
>
>
Thank you very much for your help, It is much more clearer now.

Nawel

>
> -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