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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