On 12/24/12 12:43 PM, Ankita naithani wrote:
Hi Justin,
Thank you so much for your response.
I also noticed that when I type in gmxcheck -f md.cpt to see which
version was used, I get the same fatal error of "Attempting to read a
checkpoint file of version 13 with code of version 12".
In my linux machine, the gromacs version is 4.5.5 and the one on the
cluster is also 4.5.5. I just offloaded the data from the cluster and
was trying to run the test for continuing simulation before submitting
it to the cluster for continuation.
There is a mismatch somewhere. Run any command simply with the -h flag or read
the printed information of any command invocation to see the version. Your
executables are newer than the version of Gromacs used to do the original run.
Could you please suggest me something in this regard too. I understand
that the versions would be different but my system and cluster have
the same version of gromacs. Also, is version 13 being used by
gromacs 4.6? In that case, how do we continue a simulation with that
version?
You should use a consistent version throughout. Newer versions should always be
backwards compatible, but unless you have a specific reason for upgrading
(especially between major releases), I would avoid it.
If somehow someone updated the software or switched it to gromacs 4.6
in the cluster, I will then directly invoke mdrun there but I would
need to know if the command would be the same for continuing the
simulation in gromacs 4.6?
i.e.
mdrun -cpi md.cpt -s md.tpr
The commands haven't changed in this respect. Adding -cpi -append to whatever
you ran before is sufficient to continue the simulation if everything else is
consistent.
Sorry for bothering with silly questions, my time on the cluster runs
out in 2 days so I really could do with as much help I can for now
You can always install your own version of Gromacs in a location accessible to
you, like your home directory, and run using those executables. Silently
replacing a version of software and nuking the old one is a great way to upset
users, so hopefully the other version is still available somewhere, even if not
in the default $PATH. Only your sysadmins know that, though.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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