[gmx-users] Error

[André Farias de Moura]

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