Great! Thanks. Serena
> Hi, > > I fixed the bug for 4.0.8 (if it will ever be released). > > You can work around it by put your protein in a big box and using long > cut-off's > with domain decomposition (or simple run in serial). > > The next version of Gromacs will support domain decomposition also > for vacuum simulations, even without cut-off's. > > Berk >/ Date: Wed, 20 Jan 2010 09:34:45 +0100 />/ From: sdonnin at gwdg.de <http://lists.gromacs.org/mailman/listinfo/gmx-users> />/ To: gmx-users at gromacs.org <http://lists.gromacs.org/mailman/listinfo/gmx-users> />/ Subject: [gmx-users] problem with vsite and particle decomposition />/ />/ Hi, />/ />/ yes, I've just filed a bugzilla and attached the tpr. />/ Thanks, />/ />/ Serena />/ />/ > Hi, />/ > />/ > This is clearly a bug. />/ > Could you file a bugzilla and attach the tpr file? />/ > />/ > Thanks, />/ > />/ > Berk />/ />/ >/ Date: Wed, 20 Jan 2010 08:52:27 +0100 />/ />/ From: sdonnin at gwdg.de <http://lists.gromacs.org/mailman/listinfo/gmx-users> />/ />/ To: gmx-users at gromacs.org <http://lists.gromacs.org/mailman/listinfo/gmx-users> />/ />/ Subject: [gmx-users] problem with vsite and particle decomposition />/ />/ />/ />/ Hallo, />/ />/ />/ />/ I had a problem when running with virtual sites (-vsite hydrogens) and />/ />/ particle decomposition (mdrun -pd) on more than one processor with />/ />/ gromacs 4.0.7. I could run without problems the same files without />/ />/ virtual site description. The error message looks like this: />/ />/ />/ />/ [node036:28870] *** An error occurred in MPI_Wait />/ />/ [node036:28870] *** on communicator MPI_COMM_WORLD />/ />/ [node036:28870] *** MPI_ERR_TRUNCATE: message truncated />/ />/ [node036:28870] *** MPI_ERRORS_ARE_FATAL (goodbye) />/ />/ />/ />/ It seems that the error message comes from move_cgcm() in />/ />/ sim_util.c, line 157, but the cause could as well />/ />/ be MPI communication that happens before move_cgcm. />/ />/ />/ />/ Did anybody experienced similar problems or can help with this issue? />/ />/ Thanks, />/ />/ />/ />/ Serena />/ />/ / <http://lists.gromacs.org/mailman/listinfo/gmx-users> -- 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/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/mailing_lists/users.php
