[gmx-users] Error

Fri Jun 12 17:02:37 CEST 2015

Dear Andre sir,

Thank you for your reply. I have a problem in the topology file which I
have generated and it is working fine now. Thank  you for your support.

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 Mon, Jun 8, 2015 at 11:05 AM, André Farias de Moura <moura at ufscar.br>
wrote:

> 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
> > > > --
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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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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