[gmx-users] demux.pl input file

[Nawel Mele]

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

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?

Nawel






>
>
> 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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>>> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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-- 

Nawel Mele, PhD Research Student

Jonathan Essex Group, School of Chemistry

University of Southampton,  Highfield

Southampton, SO17 1BJ