[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 10

[Mark Abraham]

Hi,

OK, that may be a bug, but I can't imagine why only you experience it.
Please file an issue at http://redmine.gromacs.org and attach (at least)
the files you're using for the restart and the commands with which you used
them.

Mark

On Wed, Dec 3, 2014 at 7:55 PM, wh <signoreguidami at 163.com> wrote:

>
>
> > >> Dear Gromacs Users,
> >
> > >>
> >
> > >>
> >
> > >>
> >
> > >> Recently when I tried to restart a md simulation from previous one
> >
> > >> using convert-tpr with version 5.0.1 , the task failed giving the
> > >> error
> > message:
> >
> > >>
> >
> > >>
> >
> > >>
> >
> > >> X particles communicated to PME node Y are more than a cell length
> > >> out
> >
> > >> of the domain decomposition cell of their charge group
> >
> > >>
> >
> > >>
> >
> > >>
> >
> > >> I tried several way to solve it, including modify the equilibration
> >
> > >> setting as it said in the gromacs error page, and all failed. If I
> >
> > >> just run one simulation for a long time, it will not crash, at
> > >> least
> >
> > >> can do further than the time point it crashed when using restart.
> >
> > >>
> >
> > >> Does anyone have any idea why this happen and how to solve it?  I
> > >> used
> >
> > >> the
> >
> > >> syntax:
> >
> > >>
> >
> > >> gmx convert-tpr -s input.tpr -f input.trr -e input.edr -o
> > >> output.tpr
> >
> > >> -extend
> >
> > >> 10000
> >
> > >>
> >
> > >> Any suggestion will be greatly appreciated
> >
> > >>
> >
> >
> >
> > >Do not supply .trr and .edr files; just increase the number of steps
> > >and
> > continue from the existing checkpoint with mdrun -cpi.  What you're
> > doing is based on ancient syntax that is no longer relevant.  I'm
> > guessing that you're probably winding up with discontinuous states
> > somehow.
> >
> >
> >
> > >
> > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Ver
> > sion_
> > 4_and_Newer
> >
> >
> >
> > >-Justin
> >
> >
> >
> > Thank you so much for your timely reply, yet I tried mdrun -s
> > input.tpr -cpi input.cpt -append
> >
> > It still gave the same error message. Could it be a bug? Or I did
> > something wrong?
>
>
> Bug is possible but unlikely. We definitely don't have enough information
> to
> tell because we've gotten half of it each time - what was the conversion
> + restart combination you actually used? Does the original run stay
> + stable
> if it is not interrupted?
>
> Mark
>
>
>
>
>
>
> If I run a long time simulation continuously it can stay stable. I just
> want
> to run it in smaller jobs or restart it from a check point because of the
> limit on computing resources. Suggested by  Justin I used syntax:
> mdrun -s input.tpr -cpi input.cpt -append, using the cpt file from the
> previous simulation yet it still gave the same error message.
>
>
> --
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