[gmx-users] error in parallel mdrun

[hazizian]

hi 

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                   

then 

> 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 
247185117020282387238658576035127661536052825745545652719669759062373813704493551571478495838644038086589824739452834743244657492619860086077032362651572801981421019014673105813372306735907332585544062133537655269329581179473829805619840403813960735860655676896572043357093782778978904568459302010880.000 
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.
thanks

--
Tehran University of Medical Sciences
www.tums.ac.ir


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