Hi, I ran some MD simulations (NPT ensemble) and a series of simulations to determine the free energy of water solvation of a not to big molecule.
I noticed that while I was able to run the MD simulations using all the CPUs (or threads) in my workstation (12 CPUs or 24 threads, respectively), whereas during free energy I can use 2 CPUs at most. If I try to use more, the simulations would crash stating: Program mdrun, VERSION 4.6.3 Source code file: /home/zidar/utils/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792 Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 4.52667 nm Change the number of nodes or mdrun option -rdd or -dds 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 can use more CPUs only if I switch from domain decomposition to particle decomposition scheme. The size of the systems evaluated is 11.92513nm x 5.44212nm x 5.35234nm with ~30.000 atoms, so I assume the size of the system is not an issue. Big question: Why is that so? Why can I use more CPUs for 'regular' MD but only two for free energy simulations? I'd really like to use more CPUs as it would really speed-up the simulations. Thanks in advance, Jernej Zidar -- 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
