Hi, Tsjerk, does it make sense to try to have grompp observe the particle density and guide the default of -rdd accordingly?
Mark On Wed, Mar 23, 2016 at 9:19 AM Tsjerk Wassenaar <[email protected]> wrote: > Hi James, > > Try setting -rdd 1.4 in mdrun. Sometimes 1.5 or 1.6 is necessary > (especially if you use a larger time step, like 30 fs). > > Cheers, > > Tsjerk > On Mar 23, 2016 09:08, "James Starlight" <[email protected]> wrote: > > > Hello, > > > > > > I am trying to perform 2 MARTINI simulations of several membrane > > receptors within membrane i) with eldyn restrains applied on the > > protein tetriary structure and ii) unrestrained md. I have no problems > > in the i) case but in the ii) my simulation is very unstable under > > pruduction run- it begins OK after long period of equilibration but > > suddenly is crashed after 20-50ns of C run although I reduced the > > integration time-step twisely in comparison to restrained run (0.005 > > vs 0.01) > > > > Fatal error: > > 1 of the 20932 bonded interactions could not be calculated because > > some atoms involved moved further apart than the multi-body cut-off > > distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see > > option -rdd, for pairs and tabulated bonds also see option -ddcheck > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > > > might another tricks be used here besides elastic restraints consisted > > of mostly of md simulation setups e.g switching to the another > > termostat (right now martini uses berendsen with gmx 4.5) e.g ussing > > of sd integraator instead7 > > > > Thanks for help! > > > > James > > -- > > 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]. > -- 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].
