<div class="gmail_quote">On Fri, Jul 15, 2011 at 1:41 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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On 15/07/2011 7:31 PM, Martin Kamp Jensen wrote:
<blockquote type="cite"><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">Hello,
<div><br>
</div>
<div>I am trying to evaluate energy values of several
conformations using a (pseudo)trajectory. Currently, I am
concatenating GROMOS-96 files (.g96) and using that as a
trajectory. For some reason the second conformation in a
trajectory is ignored. So e.g. if I have three conformations
(1.g96, 2.g96, and 3.g96), then concatenate them into
1+2+3.g96, and then use the latter file as a trajectory, the
conformation of 2.g96 is ignored when using mdrun -rerun with
a suitable binary run file.</div>
<div><br>
</div>
<div>I have created an archive [1] with files demonstrating the
problem. Use the "run" script for a stepwise demonstration of
the problem: The output of mdrun shows that the last frame
processed is one less then expected for concatenated files.
Further, it is the second frame that is missing which can be
determined by looking at the energy values in the energy file
generated by mdrun.</div>
<div><br>
</div>
</span><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">I
have no clue what is going on here. I hope someone can provide
some insights. </span><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">(The same approach seems to work fine with PDB
files instead of GROMOS-96 files, but there is less precision in
PDB files and because of some irrelevant details it is easier
for me to work with GROMOS-96 files at the moment.)</span><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">
<div>
<br>
</div>
</span><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">[1] <a href="http://dl.dropbox.com/u/2666968/GROMACS/missingframe.tar" target="_blank">http://dl.dropbox.com/u/2666968/GROMACS/missingframe.tar</a></span>
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<div>
Thanks,</div>
<div>Martin.</div>
</span></div>
</blockquote>
<br></div></div>
That's a bug. Reading the .g96 file format as a trajectory uses some
dirty dirty non-thread-safe code, and the cleanup a few years ago to
make things thread-safe did that without preserving correct
functionality. I suggest you concatenate separate .g96 files using
trjcat into .trr format, and use rerun on that.<br></div></blockquote><div><br></div><div>Too bad, but thank you for explaining. Is your suggestion based on the fact that the functionality is completely unreliable? I mean, if the bugs are known (e.g. 2nd frame is always ignored), it would maybe be better to just work around them. (It would be a bit sad to write out 100 or 1000 g96 files and then use trjcat since I will need to do that millions of times during a run of my application.)</div>
<div><br></div><div>Regards,</div><div>Martin.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff">
<br>
Mark<br>
</div>
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