Hi! I am trying to run a simple MD simulation as usual, but with this system I have got the same error message:
*Fatal error:There is no domain decomposition for 160 ranks that is compatible with thegiven box and a minimum cell size of 1.02425 nmChange the number of ranks or mdrun option -rcon or -dds or your LINCSsettingsLook in the log file for details on the domain decomposition* And when looking in the log file *Initializing Domain Decomposition on 200 ranksDynamic load balancing: lockedMinimum cell size due to atom displacement: 0.476 nmInitial maximum distances in bonded interactions: two-body bonded interactions: 0.431 nm, LJ-14, atoms 1820 1827 multi-body bonded interactions: 0.431 nm, Proper Dih., atoms 1820 1827Minimum cell size due to bonded interactions: 0.474 nmMaximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nmEstimated maximum distance required for P-LINCS: 0.819 nmThis distance will limit the DD cell size, you can override this with -rconGuess for relative PME load: 0.18Will use 160 particle-particle and 40 PME only ranksThis is a guess, check the performance at the end of the log fileUsing 40 separate PME ranks, as guessed by mdrunScaling the initial minimum size with 1/0.8 (option -dds) = 1.25Optimizing the DD grid for 160 cells with a minimum initial size of 1.024 nmThe maximum allowed number of cells is: X 7 Y 7 Z 7* Those atoms are parte of a Met residue. I have no clue how to solve this or what I am having this problem. Thank you very much. Cheers, /P -- 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.
