Never mind my previous message. When I included periodicmolecule = yes in the mdp file, I believe that took care of the problem.
Thanks, Jon --------------------------------------------- Hey! I ran into an issue when simulating graphene sheets with periodic boundary conditions. It said: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 4.685 nm I figured that was due to the apparent bond length of the carbons connected across the box, so I set -rdd to be 0.2 nm and now the simulation seems to be running fine. Is the -rdd command ignoring the bonds completely for the simulation, or still using bonds across the box edges once PBC is implemented? Thank you! Jon -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
