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.
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?
Mark
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Jerome
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