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On 16/07/2011 8:33 PM, Martin Kamp Jensen wrote:
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cite="mid:CAFVEjonzxOq23=WN7xhYp9J-zuSMaL38DLppvWHLrda9+LMaXw@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Fri, Jul 15, 2011 at 1:41 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
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0.8ex; border-left: 1px solid rgb(204, 204, 204);
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<div class="h5"> 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
moz-do-not-send="true"
href="http://dl.dropbox.com/u/2666968/GROMACS/missingframe.tar"
target="_blank">http://dl.dropbox.com/u/2666968/GROMACS/missingframe.tar</a></span>
<div> <font face="arial, sans-serif"><span
style="border-collapse: collapse;"><br>
</span></font><span style="border-collapse:
collapse; font-family: arial,sans-serif;
font-size: 13px;">
<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?</div>
</div>
</blockquote>
<br>
Yes. The behaviour of the code is (in principle) unpredictable, but
you might get lucky and observe regularities, and here you did.<br>
<br>
<blockquote
cite="mid:CAFVEjonzxOq23=WN7xhYp9J-zuSMaL38DLppvWHLrda9+LMaXw@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div> I mean, if the bugs are known (e.g. 2nd frame is always
ignored), it would maybe be better to just work around them. </div>
</div>
</blockquote>
<br>
If anything, the bug will lead to skipping alternate frames. You
could try constructing the input to have empty frames, or duplicate
frames, and check the output very carefully to see patterns in what
happens.<br>
<br>
<blockquote
cite="mid:CAFVEjonzxOq23=WN7xhYp9J-zuSMaL38DLppvWHLrda9+LMaXw@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>(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>
</blockquote>
<br>
You could write .gro files if they have enough precision, or .xtc
files (there's a C library for doing the latter on the GROMACS
webpage).<br>
<br>
Mark<br>
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