Dear Mark, thanks for your answer. The version is 2016.5, but I apparently solved the problem recompiling gromacs: now the simulation is running quite stable. I had minimized and gradually equilibrated the system and I could not see any weird bonds or contacts. So in the end, as extrema ratio, I decided to recompile.
Thanks again Stefano 2018-06-22 15:07 GMT+02:00 Mark Abraham <[email protected]>: > Hi, > > This could easily be that your system is actually not yet well equilibrated > (e.g. something was trapped in a high energy state that eventually relaxed > sharply). Or it could be a code bug. What version were you using? > > Mark > > On Thu, Jun 21, 2018 at 2:36 PM Stefano Guglielmo < > [email protected]> wrote: > > > Dear users, > > > > I have installed gromacs with MPI instead of its native tMPI and I am > > encountering the following error: > > "Fatal error: > > 4 particles communicated to PME rank 5 are more than 2/3 times the > cut-off > > out > > of the domain decomposition cell of their charge group in dimension y. > > This usually means that your system is not well equilibrated." > > > > I am using 8 MPI ranks with 4 omp threads per rank (it was the > > configuration used on the same machine by tMPI), but I also tried 4 ranks > > with 8 threads, but it did not solve the problem. > > > > I don't think this is an issue related to my system because the same > system > > run with the native tMPI works properly (it has already been termalized > and > > gradually equilibrated); neverthless I tried to reduce dt and temperature > > but without any benefit. Does anybody have any suggestions? > > > > Thanks in advance > > Stefano > > > > -- > > Stefano GUGLIELMO PhD > > Assistant Professor of Medicinal Chemistry > > Department of Drug Science and Technology > > Via P. Giuria 9 > > 10125 Turin, ITALY > > ph. +39 (0)11 6707178 <011-670%2071%2078> > > -- > > 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 [email protected]. > > > -- > 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 [email protected]. > -- Stefano GUGLIELMO PhD Assistant Professor of Medicinal Chemistry Department of Drug Science and Technology Via P. Giuria 9 10125 Turin, ITALY ph. +39 (0)11 6707178 -- 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 [email protected].
