[E-Info] (utan titel)

chitrala kumaraswamynaidu cksnaidu at gmail.com
Fre Juni 5 21:13:41 CEST 2015

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,

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


Dr. Naidu
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