Hi, Nobody advocates the use of Berendsen coupling in production simulation. But it does not follow that one can only use langevin dynamics to be accurate - mdrun implements several other coupling approaches...
Mark On Wed, 23 Mar 2016 10:43 James Starlight <[email protected]> wrote: > Btw taking back to my question regarding thermostats in CG sims- does > the correct choise influence on sampling here`? E.g in full atomistic > sims generally langevens dynamics produces better results in > comparison to berendsen thermostat which produce very unphysical > behaviour for the macromolecular systems. > > J. > > 2016-03-23 10:32 GMT+01:00 Tsjerk Wassenaar <[email protected]>: > > Hi Mark, > > > > In combination with the time step and maybe the particle mass, that would > > be lovely. A dynamic update, based on the actual displacements would also > > be possible after some steps (-rdd -1 ?). > > > > Cheers, > > > > Tsjerk > > On Mar 23, 2016 09:37, "Mark Abraham" <[email protected]> wrote: > > > >> 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]. > >> > > -- > > 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].
