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
aim!
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
calculation?
gmxcheck
-Justin
Mark
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Jerome
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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