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
