[gmx-users] Error

[chitrala kumaraswamynaidu]

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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