[gmx-users] concaternating remd trajectories using trjcat & demux

[Segun Jung]

Thanks Justin,


On Wed, Feb 10, 2010 at 8:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Segun Jung wrote:
>
>> Dear gromacs users,
>>
>> I am trying to collect trajectories corresponding to each temperature by
>> using trjcat with demux.
>>
>> There were similar issues posted earlier, but I do not see the solution on
>> the problem I am facing following:
>>
>>
> Like what?  It will save time if you can post links to these "similar
> issues" to avoid posting non-solutions that have already been ruled out.
>
>
>  I have 64 replicas simulated using namd  in dcd trajectory format and
>> saved them in gromacs format (.trr) using vmd.
>>
>> I inspected the gromacs format trajectories by eyes in vmd and looked
>> fine. However, when I tried trjcat -f g*.trr -demux replica_index.xvg,
>>
>> the output looked weird. So I tested a small set of the trajectories
>> (using only replicas 0 to 8 and first two frames) and
>>
>> noticed that the output does not match to the replica_index.xvg file.
>>
>>
> If you ran your simulations with NAMD, how did you generate this file?  In
> Gromacs, one would run demux.pl on the md.log file.  I presume NAMD prints
> different output.
>
> I wrote a perl script which does the same job as demux.pl generating the
replica_index.xvg.

>
>
>> trjcat -f *g*.trr -demux replica_index.xvg
>>
>> replica_index.xvg
>>
>> 0 0 1 2 3 4 5 7 6
>>
>> 2 1 0 2 3 5 4 6 7
>>
>>
> If you analyzed replicas 0 to 8 (inclusive) then you should have an 8
> somewhere, right?


And I was testing 8 replicas (from 0 to 7).  Sorry about the confusion.

>
>
>
>> I am using Ubuntu (32bit) and the gromas version is 4.0.5.
>>
>> 0_trajout.xtc should have the 1st frame from replica 0 and 2nd frame from
>> replica 1, but both frames for 0_trajout.xtc are from the replica 0.
>>
>>
> This might go along with my comment above.  If there are nine replicas (0
> to 8), then there may be some mis-translation of the .xvg file.
>
>
>  It seems the index file does not cooperate properly with the trjcat and
>> -demux. Does anyone have clue about this?
>>
>>
> I know I can attest to demultiplexing working as advertised, so I assume
> intact trajectories with a correct index file should work properly.  You
> have a few variables to deal with: .dcd->.trr translation, however you
> generated the .xvg file, and if you've even told us the right number of
> replicas, among perhaps others.
>

I fixed a minor mistake in my perl script which generates replica_index.xvg
and it works fine except the time step 0 of input file (*.trr) is saved two
times in the output file (*.xtc) although rest of the trajectories are okay.


-Segun

>
> Also, what does gmxcheck tell you about each of the .trr files?  Do they
> contain what you would expect them to?
>
> -Justin
>
>
>> Many thanks,
>>
>> Segun
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- 
---------------------------------------
Segun Jung, Ph.D. Candidate
Computational Biology
Schlick Lab, Department of Chemistry
New York University
http://homepages.nyu.edu/~sj801
----------------------------------------
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