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 ************************************************ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
