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Dear Derrick, <br>
<br>
<br>
According to the GROMACS manual, the xtc format is a <b>compressed, portable</b>
format for trajectories, containing only coordinates, while trr is a binary,
full precision file, containing x, v and f information. The xtc uses the
<i>xdr</i> routines for writing and reading data which was created for the
Unix NFS system. The trajectories are written using a reduced precision algorithm
which works in the following way: the coordinates (in nm) are multiplied
by a scale factor, typically 1000, so that you have coordinates in pm. These
are rounded to integer values. Then several other tricks are performed, for
instance making use of the fact that atoms close in sequence are usually
close in space too (e.g. a water molecule). To this end, the <i>xdr</i> library
is extended with a special routine to write 3-D float coordinates.<br>
<pre wrap=""></pre>
I think that since xtc files contain only coordinates and are therefore significantly
smaller, they might be more suitable for import into VMD. Here is what Anton
said about writing out xtc and trr trajectories:<br>
<pre>"I use the default ndec=3, that is sufficient for all types of analysis that I ever heard of. I tune nstxout/nstvout so that a frame is written
to .trr file every few hours along the calculation (usually every 10-50ps). Depending on how much disk is on the machine I run on, I either write the whole system to .xtc every 1 ps, or I only write protein(s) + substrate(s) + co-factor(s). That, I also put on CD (or, recently, on DVD!). Then, I make one .xtc file with only the 'protein+stuff' in it (if I haven't got that
already), and a few ones with less frames, like every 10 ps and every 100ps, which I can use for quick analysis (e.g. an rmsd plot)."<br><br>Greetings,<br><br>Martina Bertsch, Ph.D.
Northwestern University
Feinberg School of Medicine
Molecular Pharmacology and Biological Chemistry
303 East Chicago Avenue
Chicago, IL 60611
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Ilya Chorny wrote:<br>
<blockquote type="cite" cite="mid:1069374901.10088.4.camel@chaos.compbio.ucsf.edu">
<pre wrap="">I'm not exactly sure what the advantage is to using the xtc vs trr. I<br>think both will work. I believe the trr output can be adjusted by<br>setting nstxout = 100. The trr files contains more info then just<br>coordinates like velocities and forces.<br><br>-x option in mdrun directs the output to a file name for the .xtc<br>output.<br><br>type mdrun -h for more info <br><br>Ilya<br><br><br> <br>On Thu, 2003-11-20 at 16:27, Derrick Guang Yuh Lee wrote:<br></pre>
<blockquote type="cite">
<pre wrap="">dear Ilya<br><br>thank you for the info, two things though. is there any advantage of<br>having VMD use the xtc file over the tjr file? and you mentioned the -x<br>option of mdrun, i'm not a hundred percent sure what you mean by that,<br>could you please be a bit more detailed about that? thanks.<br><br><br> - derrick<br><br><br> derrick Lee<br> faculty of Science<br> Memorial University of Newfoundland<br> <a class="moz-txt-link-abbreviated" href="mailto:k24dgyl@mun.ca">k24dgyl@mun.ca</a> or <a class="moz-txt-link-abbreviated" href="mailto:derrickglee@hotmail.com">derrickglee@hotmail.com</a><br><br>"a teacher is never a giver of truth - he is a guide, a pointer to the<br>truth that each student must find for himself. a good teacher is merely a<br>catalyst."<br> - bruce lee<br><br>On Thu, 20 Nov 2003, Ilya Chorny wrote:<br><br></pre>
<blockquote type="cite">
<pre wrap="">VMD can read xtc files as well. VMD reads the corrdinates it doesn't<br>need velocities.<br><br>Set<br><br>nstxtcout = 100<br><br>and don't forget the -x option in mdrun<br><br>Ilya<br><br><br>On Thu, 2003-11-20 at 15:40, Derrick Guang Yuh Lee wrote:<br></pre>
<blockquote type="cite">
<pre wrap="">dear [gmx-users]<br><br>i was just curious if someone could help me create a movie for VMD. it had<br>just occured to me that i can use my trajectory file (.tjr) to view my<br>monolayer in VMD, but because it is 1ns simulation, the file is a little<br>too large for VMD and our computers here.<br><br>so, would anyone be able to inform me of how i could set it up such that<br>my trajectory file prints out the velocities and coordinates of my system<br>about 100 times or so? it'd be appreciated. thanks.<br><br><br> - derrick<br><br> derrick Lee<br> faculty of Science<br> Memorial University of Newfoundland<br> <a class="moz-txt-link-abbreviated" href="mailto:k24dgyl@mun.ca">k24dgyl@mun.ca</a> or <a class="moz-txt-link-abbreviated" href="mailto:derrickglee@hotmail.com">derrickglee@hotmail.com</a><br><br>"a teacher is never a giver of truth - he is a guide, a pointer to the<br>truth that each student must find for himself. a good teacher is merely a<br>cataly
st."<br> - bruce lee<br><br>_______________________________________________<br>gmx-users mailing list<br><a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></pre>
</blockquote>
<pre wrap="">--<br>----------------------------------------------------------------<br>Ilya Chorny Ph.D. Department of Pharmaceutical Chemistry<br>Postdoctoral Researcher University of California-San Francisco<br>phone: (408)-887-8496 Genentech Hall 600 16th St Box 2240<br>fax: (415)502-1411 San Francisco, Ca, 94107<br> email: <a class="moz-txt-link-abbreviated" href="mailto:ichorny@maxwell.ucsf.edu">ichorny@maxwell.ucsf.edu</a><br>----------------------------------------------------------------<br><br>_______________________________________________<br>gmx-users mailing list<br><a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a class="moz-txt-link-
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<pre wrap="">_______________________________________________<br>gmx-users mailing list<br><a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></pre>
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<pre wrap=""><!----><br>_______________________________________________<br>gmx-users mailing list<br><a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br><br><br></pre>
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