[gmx-users] Error

Mon Jun 8 17:05:11 CEST 2015

NaN means "not a number" and usually it means some force went to infinity
and thus your system is exploding.

running on a larger cluster won't be of any help, you have to move one step
back and perform a proper energy minimization. if the error persists, you
should also check your topology for anything spurious leading to
energy/forces to infinity.

On Mon, Jun 8, 2015 at 11:41 AM, chitrala kumaraswamynaidu <
cksnaidu at gmail.com> wrote:

> Dear Andre sir,
>
> Thank you for your reply. I have gone through the threads but I didn't got
> the exact solution for my problem.
>
> I have run the protein-ligand system upto  nvt.tpr  mdrun execution steps
> in my laptop with Ubuntu. It is running comfortably but showing the output
> -nan. Therefore, I thought to run it on the bolden cluster in our institute
> in that it is showing the following error.
>
> Will use 108 particle-particle and 12 PME only ranks
> This is a guess, check the performance at the end of the log file
> Using 120 MPI threads
> Using 1 OpenMP thread per tMPI thread
> starting mdrun 'Protein in water'
> 50000 steps,    100.0 ps.
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.4
> Source code file: /share/apps/src/gromacs-5.0.4/src/gromacs/mdlib/pme.c,
> line:
> 7
> 54
>
> Fatal error:
> 2 particles communicated to PME rank 4 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> <
> https://uscmed.sc.edu/owa/redir.aspx?C=yM9xud_v1UCcNWWL-kM_GJgAd3dac9JI8UROBD4C7QFS8Rm-Bi1ts3jy27V4QHa_v159NARSf4A.&URL=http%3a%2f%2fwww.gromacs.org%2fDocumentation%2fErrors
> >
>
> Thank you sir once again for your valuable reply.
>
>
>
> Yours sincerely,
>
> *Dr. C.Kumaraswamy Naidu, Ph.D.*
> Post doctoral Fellow Bioinformatics,
> Department of PMI, School of Medicine,
> University of South Carolina,
> Columbia, South Carolina 29208
>
>
> On Fri, Jun 5, 2015 at 5:05 PM, André Farias de Moura <moura at ufscar.br>
> wrote:
>
> > the error message is self-explaining and provides the web link you should
> > have followed before posting here (you should also have checked the
> mailing
> > before posting, this is a recurring topic)
> >
> > On Fri, Jun 5, 2015 at 5:55 PM, chitrala kumaraswamynaidu <
> > cksnaidu at gmail.com> wrote:
> >
> > > I have run the following command on the Cluster server  and I got the
> > > following error. Can anyone Please help me why I am facing this error.
> > >
> > > gmx mdrun -deffnm nvt_2 -v
> > >
> > > Reading file nvt_2.tpr, VERSION 5.0.4 (single precision)
> > > Changing nstlist from 10 to 25, rlist from 1.4 to 1.433
> > >
> > >
> > > Will use 108 particle-particle and 12 PME only ranks
> > > This is a guess, check the performance at the end of the log file
> > > Using 120 MPI threads
> > > Using 1 OpenMP thread per tMPI thread
> > > starting mdrun 'Protein in water'
> > > 50000 steps,    100.0 ps.
> > >
> > > -------------------------------------------------------
> > > Program gmx, VERSION 5.0.4
> > > Source code file:
> /share/apps/src/gromacs-5.0.4/src/gromacs/mdlib/pme.c,
> > > line:
> > > 7
> > > 54
> > >
> > > Fatal error:
> > > 2 particles communicated to PME rank 4 are more than 2/3 times the
> > cut-off
> > > out of the domain decomposition cell of their charge group in dimension
> > x.
> > > This usually means that your system is not well equilibrated.
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > > <
> > >
> >
> https://uscmed.sc.edu/owa/redir.aspx?C=yM9xud_v1UCcNWWL-kM_GJgAd3dac9JI8UROBD4C7QFS8Rm-Bi1ts3jy27V4QHa_v159NARSf4A.&URL=http%3a%2f%2fwww.gromacs.org%2fDocumentation%2fErrors
> > > >
> > >
> > >  regards,
> > >
> > > Dr. Naidu
> > > --
> > > Gromacs Users mailing list
> > >
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> > >
> >
> >
> >
> > --
> > _____________
> >
> > Prof. Dr. André Farias de Moura
> > Department of Chemistry
> > Federal University of São Carlos
> > São Carlos - Brazil
> > phone: +55-16-3351-8090
> > --
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090