Could be a bug, but unless you can reproduce it with 4.5.7 or 4.6.x then you won't get much help there :-)
Mark On Fri, May 31, 2013 at 9:56 PM, Parker de Waal <parker.dewaa...@kzoo.edu>wrote: > Hi Everyone, > > I'm trying to run energy minimization on my system and I am encountering > the following error: > > Getting Loaded... > Reading file em.tpr, VERSION 4.5.5 (single precision) > Starting 16 threads > Loaded with Money > > > Will use 10 particle-particle and 6 PME only nodes > This is a guess, check the performance at the end of the log file > > ------------------------------------------------------- > Program mdrun, VERSION 4.5.5 > Source code file: domdec.c, line: 6436 > > Fatal error: > There is no domain decomposition for 10 nodes that is compatible with the > given box and a minimum cell size of 9.07242 nm > Change the number of nodes or mdrun option -rdd > Look in the log file for details on the domain decomposition > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > I've tested my bash script on a local server with an i7 and I've been able > to run error free, however when running on xsede resources I continually > encounter this error. > > For information here is my bash: > #minimization > grompp -f minim.mdp -c protein_solv_ions.gro -p protein.top -o em.tpr > mdrun -v -deffnm em > if [ ! $? == 0 ] > then > echo "ERROR - Energy minimization" > exit 5 > fi > > and Here is my minim.mdp > > integrator = steep > emtol = 10 > emstep = 0.01 > nsteps = 200 > energygrps = System > > nstlist = 5 > ns_type = grid > rlist = 1.0 > coulombtype = PME > rcoulomb = 1.0 > rvdw = 1.0 > pbc = xyz > > Any input would help! > > Thanks, > Parker > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists