Hi, I am a newbie in Gromacs and is trying to simulate a small organic molecule in water. I got the following error message during a position restrained md run. I tried changing number of nodes but without success.
Any help on this is appreciated. Initializing Domain Decomposition on 16 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.400 nm, LJ-14, atoms 10 14 multi-body bonded interactions: 0.400 nm, Ryckaert-Bell., atoms 10 14 Minimum cell size due to bonded interactions: 0.440 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.761 nm Estimated maximum distance required for P-LINCS: 0.761 nm This distance will limit the DD cell size, you can override this with -rcon Guess for relative PME load: 0.21 Will use 12 particle-particle and 4 PME only nodes This is a guess, check the performance at the end of the log file Using 4 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 12 cells with a minimum initial size of 0.951 nm The maximum allowed number of cells is: X 2 Y 2 Z 2 ------------------------------------------------------- Program mdrun_mpi_d, VERSION 4.5.5 Source code file: domdec.c, line: 6436 Fatal error: There is no domain decomposition for 12 nodes that is compatible with the given box and a minimum cell size of 0.95125 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings 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 ------------------------------------------------------- -best, Dipankar Roy -- 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