Thanks Justin,<br><br><br><div class="gmail_quote">On Wed, Feb 10, 2010 at 8:49 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Segun Jung wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear gromacs users,<br>
<br>
I am trying to collect trajectories corresponding to each temperature by using trjcat with demux.<br>
<br>
There were similar issues posted earlier, but I do not see the solution on the problem I am facing following:<br>
<br>
</blockquote>
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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.<div class="im"><br></div></blockquote><div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I have 64 replicas simulated using namd in dcd trajectory format and saved them in gromacs format (.trr) using vmd.<br>
<br>
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,<br>
<br>
the output looked weird. So I tested a small set of the trajectories (using only replicas 0 to 8 and first two frames) and<br>
<br>
noticed that the output does not match to the replica_index.xvg file.<br>
<br>
</blockquote>
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If you ran your simulations with NAMD, how did you generate this file? In Gromacs, one would run <a href="http://demux.pl" target="_blank">demux.pl</a> on the md.log file. I presume NAMD prints different output.<div class="im">
<br></div></blockquote><div>I wrote a perl script which does the same job as <a href="http://demux.pl">demux.pl</a> generating the replica_index.xvg. <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
trjcat -f *g*.trr -demux replica_index.xvg<br>
<br>
replica_index.xvg<br>
<br>
0 0 1 2 3 4 5 7 6<br>
<br>
2 1 0 2 3 5 4 6 7<br>
<br>
</blockquote>
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If you analyzed replicas 0 to 8 (inclusive) then you should have an 8 somewhere, right?</blockquote><div><br>And I was testing 8 replicas (from 0 to 7). Sorry about the confusion.
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
I am using Ubuntu (32bit) and the gromas version is 4.0.5.<br>
<br>
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.<br>
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</blockquote>
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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.<div class="im"><br>
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<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
It seems the index file does not cooperate properly with the trjcat and -demux. Does anyone have clue about this?<br>
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</blockquote>
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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.<br>
</blockquote><div><br>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. <br>
<br>-Segun<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Also, what does gmxcheck tell you about each of the .trr files? Do they contain what you would expect them to?<br>
<br>
-Justin<br>
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<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Many thanks,<br>
<br>
Segun<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>---------------------------------------<br>Segun Jung, Ph.D. Candidate <br>Computational Biology <br>Schlick Lab, Department of Chemistry<br>New York University<br>
<a href="http://homepages.nyu.edu/~sj801">http://homepages.nyu.edu/~sj801</a> <br>----------------------------------------<br>