[gmx-users] Re: Continuing a simulation plus another error
jalemkul at vt.edu
Mon Dec 24 18:49:59 CET 2012
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
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?
> 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
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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