1) I guess Langevins used as thermostat works good as some kind of imitation of thermal motion produced by collisions of atoms with virtual particles in case when we modify tau_t depending of what kind of system we simulate e,g protein in water or in membrane. Why such algorithm produce wrong dynamical properties
2) I also been surpriced why in a lot of recent papers focused on GPCR modeling people used Berendsen tcoupling method instead of Nose'Hover or V-rescale for instance. J. 2016-03-23 13:15 GMT+01:00 Tsjerk Wassenaar <[email protected]>: > Hmm, the first one ends the abstract with > > "Correct dynamical properties, at least those studied in this paper, are > obtained with the Berendsen thermostat applied globally, despite the fact > that it yields the wrong kinetic energy distribution." > > So what does (un)physical mean in this respect, in relation to Berendsen, > Langevin, and other coupling methods? Is giving the wrong dynamical > properties (like Langevin) still physical? Or is a correct distribution of > kinetic energy more physical than failing on dynamical properties? > > Cheers, > > Tsjerk > On Mar 23, 2016 12:13, "Mark Abraham" <[email protected]> wrote: > >> Hi, >> >> e.g. http://pubs.acs.org/doi/abs/10.1021/ct400109a and >> http://pubs.acs.org/doi/abs/10.1021/ct300688p >> >> Mark >> >> On Wed, Mar 23, 2016 at 12:00 PM Xavier Periole <[email protected]> wrote: >> >> > >> > Any reference to illustrate the unphysical behavior of macromolecular >> > systems using Berendsen thermostat compare to others? >> > >> > XAvier. >> > >> > > On Mar 23, 2016, at 10:42, 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? 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