[gmx-users] error in parallel mdrun

[Jochen Hub]

hazizian wrote:
> 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,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

That is what is probably happening. check your starting structure and to
an energy minimization.

Best, Jochen



> 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
> 
> 


-- 
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************