[gmx-users] elastic restraints in MARTINI simulation

[Mark Abraham]

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 <jmsstarlight at gmail.com> 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 <tsjerkw at gmail.com>:
> > 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" <mark.j.abraham at gmail.com> 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 <tsjerkw at gmail.com>
> >> 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" <jmsstarlight at gmail.com>
> 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
> >> > > --
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