4.5 can only handle about 500-1000 atoms per processor. Details vary. Mark On Oct 17, 2013 5:39 AM, "Nilesh Dhumal" <ndhu...@andrew.cmu.edu> wrote:
> Thanks for you reply. > > I am doing simulation for ionic liquids BMIM + CL. Total number of atoms > are 3328. > > Nilesh > > > Assuming you're using LINCS, from the manual: > > "With domain decomposition, the cell size is limited by the distance > > spanned by *lincs-order*+1 constraints." > > Assuming a default lincs-order (4), 0.82nm seems a fairly sane distance > > for > > 5 bonds. > > > > Which means that you're probably using too many nodes for the size of > your > > system. > > > > Hope that helps. If it doesn't you'll need to provide some information > > about your system. > > > > -Trayder > > > > > > > > On Thu, Oct 17, 2013 at 1:27 PM, Nilesh Dhumal > > <ndhu...@andrew.cmu.edu>wrote: > > > >> Hello, > >> > >> I am getting the following error for simulation. I am using Gromacs > >> VERSION 4.5.5 and running on 24 processors. > >> > >> Should I reduce the number of processor or the problem is in bonded > >> parameters. If I use -nt 1 option. I could run the simulation. > >> > >> Fatal error: > >> There is no domain decomposition for 16 nodes that is compatible with > >> the > >> given box and a minimum cell size of 0.826223 nm > >> Change the number of nodes or mdrun option -rdd or -dds > >> Look in the log file for details on the domain decomposition > >> > >> > >> Nilesh > >> > >> -- > >> 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 > >> > > -- > > 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 > > > > > -- > 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 > -- 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
