[gmx-users] 3 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group

[Joanne Martin]

Hi im trying to run an NVT equilibration, and im getting the following
errors
these are my commands for solvating the box...........
any suggestions would be greatly appreciated
J

editconf -f 2VVSET_complex.gro -o 2VVSET_complex_conf.gro -box 12
genbox -cp 2VVSET_complex_conf.gro -cs
/programs/gromacs-4.0.4/share/gromacs/top/ffamber_tip3p -o
2VVSET_complex_SOL.gro -p 2VVS_complex.top

output

starting mdrun 'Protein in water'
200000 steps,    400.0 ps.
Warning: 1-4 interaction between 4346 and 4350 at distance 3.066 which is
larger than the 1-4 table size 1.900 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
MPI Application rank 19 killed before MPI_Finalize() with signal 11
MPI Application rank 17 killed before MPI_Finalize() with signal 11

-------------------------------------------------------
Program mdrun_mpi4.0.4, VERSION 4.0.4
Source code file: pme.c, line: 518

Fatal error:
3 particles communicated to PME node 7 are more than a cell length out of
the domain decomposition cell of their charge group
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