Hi, You have a bonded interaction at a distance of 10 nm. I assume that's not your intention. Perhaps you should give a configuration to grompp that has whole molecules. IIRC less ancient versions of GROMACS do a better job of this.
Mark On Thu, Feb 15, 2018 at 5:39 PM Iman Ahmadabadi <imanahmadabad...@gmail.com> wrote: > Dear Gromacs Users, > > In one job, I always get in (any number of nodes) the domain decomposition > error as following and I don't know what should I do. I have to use the > -dds or -rdd setting for my problem? > > Sincerely > Iman > > Initializing Domain Decomposition on 56 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: 9.579 nm, LJ-14, atoms 1663 1728 > multi-body bonded interactions: 9.579 nm, Angle, atoms 1727 1728 > Minimum cell size due to bonded interactions: 10.537 nm > Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.700 nm > Estimated maximum distance required for P-LINCS: 0.700 nm > Guess for relative PME load: 0.87 > Using 0 separate PME nodes, as guessed by mdrun > Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 > Optimizing the DD grid for 56 cells with a minimum initial size of 13.171 > nm > The maximum allowed number of cells is: X 0 Y 0 Z 0 > > ------------------------------------------------------- > Program mdrun, VERSION 4.6 > Source code file: /share/apps/gromacs/gromacs-4.6/src/mdlib/domdec.c, line: > 6767 > > Fatal error: > There is no domain decomposition for 56 nodes that is compatible with the > given box and a minimum cell size of 13.1712 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 > ------------------------------------------------------- > -- > 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. > -- 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.