[gmx-users] mdrun -c option "did not work"
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 26 13:25:32 CEST 2009
Jérôme Baffreau wrote:
> Thanks for your answer.
>>> Actually no my run did not finish normally the first time (it has
>>> been stopped after 7 days because of the time limitation on the
>>> cluster it was running on). So I started it again (I ran the same
>>> command and added the option "-append yes") and this time the
>>> calculation finished normally, but when I look at the md.log file it
>>> looks like the second run did not add anything since it stops in the
>>> middle of a line (in the middle of a word actually!)...
>> Sounds like a filesystem problem.
> No, that's because the Linux cluster's system terminated my calculation
> when it reached max. allowed time.
Did you supply an appropriate checkpoint file to continue the calculation?
>>> Maybe I just did not use the correct command to start this
>>> calculation again, that would explain the end of the md.log and the
>>> "no-generation" of the final structure.
>>> What option(s) should I use with trjconv? Actually I already tried to
>>> use this command, but it generated a 200 MB pdb file which was not my
>> Read trjconv -h and see how to choose the only final frame.
> I have a stupid question: how do I know how many frames there are in my
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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