Hi im trying to run an NVT equilibration, and im getting the following errors<br>these are my commands for solvating the box...........<br>any suggestions would be greatly appreciated<br>J<br><br>editconf -f 2VVSET_complex.gro -o 2VVSET_complex_conf.gro -box 12 <br>
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<br><br>output<br> <br>starting mdrun 'Protein in water'<br>200000 steps, 400.0 ps.<br>
Warning: 1-4 interaction between 4346 and 4350 at distance 3.066 which is larger than the 1-4 table size 1.900 nm<br>These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br>
or with user tables increase the table size<br>MPI Application rank 19 killed before MPI_Finalize() with signal 11<br>MPI Application rank 17 killed before MPI_Finalize() with signal 11<br><br>-------------------------------------------------------<br>
Program mdrun_mpi4.0.4, VERSION 4.0.4<br>Source code file: pme.c, line: 518<br><br>Fatal error:<br>3 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group<br>
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