<div>Hi Christopher,</div><div>you can try to use the program gmx_rescue, by Marc Baaden to recovery your trajectory.</div><div><br></div><div>Below there is the adderess:</div><a href="http://baaden.free.fr/soft/compchem.html">http://baaden.free.fr/soft/compchem.html</a><br>
<br>Francesco<div><br><div class="gmail_quote">2012/6/9 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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On 9/06/2012 7:27 AM, Christopher Neale wrote:
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Dear Users:
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</div>
<div>I have a 500 ns trajectory of 65 GB that gives a floating
point exception when I run it through gmxcheck or trjcat
(generated and analyzed with gromacs 4.5.5). Has anybody
encountered this? I ran mdrun with -append so this is the xtc
resulting from months of simulation of a 1,000,000 atom
system. If I run trjconv -f md.xtc -b 200000, where the
floating point exception occurred around t=180000 ps in
gmxcheck, then I can extract the readable frames and repair
around the damaged section. Still, I'd rather not lose any
data and I had thought that the new default -append option to
mdrun checked for these types of problems at runtime.</div>
<br>
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I've no idea what might happen when some file-system transient
occurs mid-simulation, but if mdrun has managed to compute a
checksum on an incomplete file and stored that in the checkpoint,
then the append mechanism can be none the wiser. The check upon
restart is that the checksum matches, not that the checksum is
computed on a file whose properties would satisfy gmxcheck.<br>
<br>
Note also that some file systems that do not support file locking
and this is known to cause issues (Redmine 924), but I don't know if
this is related to your observation.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
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<br>--<br>
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