Re: [gmx-users] demux.pl

[Mark Abraham]

Hi,

IIRC there's not intended to be any difference - you should be able to make
idempotent round-trips by using two rounds of trjcat with the respective
.xvg files. This is potentially useful for large simulation sets where you
don't want to have to store the original trajectories (in case you need
them) and the demuxed ones (because you're using them). But the script
isn't regularly tested, so I would not delete my primary data on the
assumption that it works perfectly...

Mark

On Tue, Oct 11, 2016 at 4:21 PM YanhuaOuyang <15901283...@163.com> wrote:

> Hi,
> I have 60 replicas simulated with REMD using gromacs. I demultiplex .xtc
> files with demux.pl script. I know we can generate a continue coordinate
> trajectory using "gmx trjcat" combined with "-demux replica_index.xvg"
> option. However I am confused with using the option "-demux
> replica_temp.xvg"  to deal with .xtc files.
>  What kind of trajectories we can get with "-demux replica_temp.xvg", are
> they coordinates at the same temperature?
> Whats the difference between trajectories generated with "-demux
> replica_temp.xvg" and the original output trajectories?
>
> Best regards,
> Ouyang
> --
> Gromacs Users mailing list
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[gmx-users] demux.pl

[YanhuaOuyang]

Hi,
I have 60 replicas simulated with REMD using gromacs. I demultiplex .xtc files 
with demux.pl script. I know we can generate a continue coordinate trajectory 
using "gmx trjcat" combined with "-demux replica_index.xvg" option. However I 
am confused with using the option "-demux replica_temp.xvg"  to deal with .xtc 
files.
 What kind of trajectories we can get with "-demux replica_temp.xvg", are they 
coordinates at the same temperature?
Whats the difference between trajectories generated with "-demux 
replica_temp.xvg" and the original output trajectories?

Best regards,
Ouyang
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Re: [gmx-users] demux.pl input file

[Nawel Mele]

2015-09-02 21:38 GMT+01:00 Justin Lemkul :

>
>
> On 9/2/15 9:21 AM, Nawel Mele wrote:
>
>> 2015-09-02 14:09 GMT+01:00 Justin Lemkul :
>>
>>
>>>
>>> On 9/2/15 8:48 AM, Nawel Mele wrote:
>>>
>>> 2015-09-02 13:38 GMT+01:00 Justin Lemkul :



> 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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441

Re: [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 :




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


2015-09-02 13:38 GMT+01:00 Justin Lemkul :




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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Gromacs Users mailing list

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Re: [gmx-users] demux.pl input file

[Andrea Pérez-Villa]

Dear Nawel,
You need to concatenate the log files of replica "0".
Regards,

Andrea

2015-09-02 12:16 GMT+02:00 Nawel Mele :

> Dear Users,
>
> I have performed a REMD simulation on a protein with 48 replicas. I have
> 400ns of REMD simulation and by consequence several restart simulation and
> so several .log files:
>
> run1_0.log , run1_0.log  run1_47.log
> run2_0.log , run2_0.log  run2_47.log
> .
> .
> .
> runx_0.log , runx_0.log  runx_47.log
>
> I am interested on the lowest temperature trajectory and I want to use the
> demux.pl scriot.
> I have been through many similar questions in the forum but I am still
> confused how to use the demux.pl script.
> Should I need to concatenate all my log files like this:
>
> cat   run1_1.log run2_1.log  ... runx_1.log   > run_total.log
>
> cat   run1_0.log run1_1.log run1_2.log...run1_47.log
> run2_0.log run2_1.log run2_2.log...   run2_47.log  ...
> runx_0.log runx_1.log runx_2.log ...runx_47.log  > run_total.log
>
> Many thanks for your help.
>
> Nawel
>
>
>
>
>
> --
>
> Nawel Mele, PhD Research Student
>
> Jonathan Essex Group, School of Chemistry
>
> University of Southampton,  Highfield
>
> Southampton, SO17 1BJ
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Andrea Pérez Villa
*"Res non Verba"*
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Re: [gmx-users] demux.pl input file

[Nawel Mele]

Dear Andrea,

Thank you very much for your quick answer.

I would like to ask you another quick question. Like I said I am interested
on a particular temperature , so I wanted to use the demux.pl file to
follow the trajectory of my temperature of interest through the temperature
space.
But, if I want the trajectory of this specific temperature in order to
perform different analysis on it like dihedral and hydrogen bond analysis.
Should I use first demux.pl on the replica "0" (for the lowest temperature)
and then use the replica_index.xvg output file and perform : trjcat -f
*.trr -demux replica_index.xvg or because during gromacs REMD simulation
only coordinates are exchanges do I need to use the demux.pl script for
extracting my trajectory??

Thanks again,

Nawel


2015-09-02 11:26 GMT+01:00 Andrea Pérez-Villa :

> Dear Nawel,
> You need to concatenate the log files of replica "0".
> Regards,
>
> Andrea
>
> 2015-09-02 12:16 GMT+02:00 Nawel Mele :
>
> > Dear Users,
> >
> > I have performed a REMD simulation on a protein with 48 replicas. I have
> > 400ns of REMD simulation and by consequence several restart simulation
> and
> > so several .log files:
> >
> > run1_0.log , run1_0.log  run1_47.log
> > run2_0.log , run2_0.log  run2_47.log
> > .
> > .
> > .
> > runx_0.log , runx_0.log  runx_47.log
> >
> > I am interested on the lowest temperature trajectory and I want to use
> the
> > demux.pl scriot.
> > I have been through many similar questions in the forum but I am still
> > confused how to use the demux.pl script.
> > Should I need to concatenate all my log files like this:
> >
> > cat   run1_1.log run2_1.log  ... runx_1.log   > run_total.log
> >
> > cat   run1_0.log run1_1.log run1_2.log...run1_47.log
> > run2_0.log run2_1.log run2_2.log...   run2_47.log  ...
> > runx_0.log runx_1.log runx_2.log ...runx_47.log  > run_total.log
> >
> > Many thanks for your help.
> >
> > Nawel
> >
> >
> >
> >
> >
> > --
> >
> > Nawel Mele, PhD Research Student
> >
> > Jonathan Essex Group, School of Chemistry
> >
> > University of Southampton,  Highfield
> >
> > Southampton, SO17 1BJ
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Andrea Pérez Villa
> *"Res non Verba"*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.




-- 

Nawel Mele, PhD Research Student

Jonathan Essex Group, School of Chemistry

University of Southampton,  Highfield

Southampton, SO17 1BJ
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[gmx-users] demux.pl input file

[Nawel Mele]

Dear Users,

I have performed a REMD simulation on a protein with 48 replicas. I have
400ns of REMD simulation and by consequence several restart simulation and
so several .log files:

run1_0.log , run1_0.log  run1_47.log
run2_0.log , run2_0.log  run2_47.log
.
.
.
runx_0.log , runx_0.log  runx_47.log

I am interested on the lowest temperature trajectory and I want to use the
demux.pl scriot.
I have been through many similar questions in the forum but I am still
confused how to use the demux.pl script.
Should I need to concatenate all my log files like this:

cat   run1_1.log run2_1.log  ... runx_1.log   > run_total.log

cat   run1_0.log run1_1.log run1_2.log...run1_47.log
run2_0.log run2_1.log run2_2.log...   run2_47.log  ...
runx_0.log runx_1.log runx_2.log ...runx_47.log  > run_total.log

Many thanks for your help.

Nawel





-- 

Nawel Mele, PhD Research Student

Jonathan Essex Group, School of Chemistry

University of Southampton,  Highfield

Southampton, SO17 1BJ
-- 
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* Please search the archive at 
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Re: [gmx-users] demux.pl input file

[Justin Lemkul]

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

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] demux.pl input file

[Justin Lemkul]

On 9/2/15 6:35 AM, Nawel Mele wrote:

Dear Andrea,

Thank you very much for your quick answer.

I would like to ask you another quick question. Like I said I am interested
on a particular temperature , so I wanted to use the demux.pl file to
follow the trajectory of my temperature of interest through the temperature
space.
But, if I want the trajectory of this specific temperature in order to
perform different analysis on it like dihedral and hydrogen bond analysis.
Should I use first demux.pl on the replica "0" (for the lowest temperature)
and then use the replica_index.xvg output file and perform : trjcat -f
*.trr -demux replica_index.xvg or because during gromacs REMD simulation
only coordinates are exchanges do I need to use the demux.pl script for
extracting my trajectory??



GROMACS trajectory and energy files are continuous in temperature, so you do not 
need demux.pl to analyze a the properties at a particular temperature. If you 
want to follow a particular structure through temperature space, you need 
demux.pl.  Any .log file should tell you about the exchanges; demux.pl simply 
reads this information to write the appropriate output files to determine how to 
follow a given structure through temperature space.


-Justin


Thanks again,

Nawel


2015-09-02 11:26 GMT+01:00 Andrea Pérez-Villa :


Dear Nawel,
You need to concatenate the log files of replica "0".
Regards,

Andrea

2015-09-02 12:16 GMT+02:00 Nawel Mele :


Dear Users,

I have performed a REMD simulation on a protein with 48 replicas. I have
400ns of REMD simulation and by consequence several restart simulation

and

so several .log files:

run1_0.log , run1_0.log  run1_47.log
run2_0.log , run2_0.log  run2_47.log
.
.
.
runx_0.log , runx_0.log  runx_47.log

I am interested on the lowest temperature trajectory and I want to use

the

demux.pl scriot.
I have been through many similar questions in the forum but I am still
confused how to use the demux.pl script.
Should I need to concatenate all my log files like this:

cat   run1_1.log run2_1.log  ... runx_1.log   > run_total.log

cat   run1_0.log run1_1.log run1_2.log...run1_47.log
run2_0.log run2_1.log run2_2.log...   run2_47.log  ...
runx_0.log runx_1.log runx_2.log ...runx_47.log  > run_total.log

Many thanks for your help.

Nawel





--

Nawel Mele, PhD Research Student

Jonathan Essex Group, School of Chemistry

University of Southampton,  Highfield

Southampton, SO17 1BJ
--
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--
Andrea Pérez Villa
*"Res non Verba"*
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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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] demux.pl input file

[Nawel Mele]

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.

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
replica_temp.xvg file from the demux.pl file to evaluate if the lowest
temperature go through all temperature space is incorrect ??  Should I
create my own script with the *_0.log file to follow the temperature
trajectory through temperature space?

Thank you very much,

Nawel


2015-09-02 13:15 GMT+01:00 Justin Lemkul :

>
>
> On 9/2/15 6:35 AM, Nawel Mele wrote:
>
>> Dear Andrea,
>>
>> Thank you very much for your quick answer.
>>
>> I would like to ask you another quick question. Like I said I am
>> interested
>> on a particular temperature , so I wanted to use the demux.pl file to
>> follow the trajectory of my temperature of interest through the
>> temperature
>> space.
>> But, if I want the trajectory of this specific temperature in order to
>> perform different analysis on it like dihedral and hydrogen bond analysis.
>> Should I use first demux.pl on the replica "0" (for the lowest
>> temperature)
>> and then use the replica_index.xvg output file and perform : trjcat -f
>> *.trr -demux replica_index.xvg or because during gromacs REMD simulation
>> only coordinates are exchanges do I need to use the demux.pl script for
>> extracting my trajectory??
>>
>>
> GROMACS trajectory and energy files are continuous in temperature, so you
> do not need demux.pl to analyze a the properties at a particular
> temperature. If you want to follow a particular structure through
> temperature space, you need demux.pl.  Any .log file should tell you
> about the exchanges; demux.pl simply reads this information to write the
> appropriate output files to determine how to follow a given structure
> through temperature space.
>
> -Justin
>
>
> Thanks again,
>>
>> Nawel
>>
>>
>> 2015-09-02 11:26 GMT+01:00 Andrea Pérez-Villa :
>>
>> Dear Nawel,
>>> You need to concatenate the log files of replica "0".
>>> Regards,
>>>
>>> Andrea
>>>
>>> 2015-09-02 12:16 GMT+02:00 Nawel Mele :
>>>
>>> Dear Users,

 I have performed a REMD simulation on a protein with 48 replicas. I have
 400ns of REMD simulation and by consequence several restart simulation

>>> and
>>>
 so several .log files:

 run1_0.log , run1_0.log  run1_47.log
 run2_0.log , run2_0.log  run2_47.log
 .
 .
 .
 runx_0.log , runx_0.log  runx_47.log

 I am interested on the lowest temperature trajectory and I want to use

>>> the
>>>
 demux.pl scriot.
 I have been through many similar questions in the forum but I am still
 confused how to use the demux.pl script.
 Should I need to concatenate all my log files like this:

 cat   run1_1.log run2_1.log  ... runx_1.log   > run_total.log

 cat   run1_0.log run1_1.log run1_2.log...run1_47.log
 run2_0.log run2_1.log run2_2.log...   run2_47.log  ...
 runx_0.log runx_1.log runx_2.log ...runx_47.log  > run_total.log

 Many thanks for your help.

 Nawel





 --

 Nawel Mele, PhD Research Student

 Jonathan Essex Group, School of Chemistry

 University of Southampton,  Highfield

 Southampton, SO17 1BJ
 --
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 posting!

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>>>
>>>
>>> --
>>> Andrea Pérez Villa
>>> *"Res non Verba"*
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>
>>
>>
>>
>>
> --
> ==
>
> 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
>
> 

Re: [gmx-users] demux.pl input file

[Nawel Mele]

2015-09-02 13:38 GMT+01:00 Justin Lemkul :

>
>
> 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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 

Nawel Mele, PhD Research Student

Jonathan Essex Group, School of Chemistry

University of Southampton,  Highfield

Southampton, SO17 1BJ
-- 
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Re: [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 :




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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at
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posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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send a mail to gmx-users-requ...@gromacs.org.







--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] demux.pl input file

[Nawel Mele]

2015-09-02 14:09 GMT+01:00 Justin Lemkul :

>
>
> On 9/2/15 8:48 AM, Nawel Mele wrote:
>
>> 2015-09-02 13:38 GMT+01:00 Justin Lemkul :
>>
>>
>>>
>>> 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
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow