[gmx-users] error in parallel mdrun

hazizian hazizian at razi.tums.ac.ir
Mon Dec 8 10:36:01 CET 2008


I want to use mdrun, when i use It as one job it goes on.
but when i use as parallel job

> grompp -np 4 -f md300.mdp -c pr.pdb -p topol.top -o md300.tpr                   


> mpirun -np 4 mdrungromacs_mpi -nice 0 -v -s md300.tpr -o md300.trr -c 
md300.pdb -e md300.edr -g md300.log

the following error apear:

starting mdrun 'SWISS-MODEL SERVER (http:'
100000000 steps,  10000.0 ps.

step 0
Warning: 1-4 interaction between 1 and 8 at distance 
which is larger than the 1-4 table size 1.000 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

Program mdrungromacs_mpi, VERSION 3.3.3
Source code file: nsgrid.c, line: 220

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.


"Everything Must Go" (Red Hot Chili Peppers)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrungromacs_mpi on CPU 0 out of 4

any help would be appriciated.

Tehran University of Medical Sciences

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