I'm trying to run a kinase (what means that I had ATP - large charged group) energy minimization and then MD.
But when I put my protein together with its ligands I gotcha the follow error message: "There is no domain decomposition for 6 nodes that is compatible with the given box and a minimum cell size of 6.47943 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition" I read about in gromacs forums and I can force the thing's running with the option nt 1 (one node...). My problem is that I still want to run in parallel. Is it still that possible for my system or I'm doomed to the 1 core simulation -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
