[gmx-users] elastic restraints in MARTINI simulation

[Tsjerk Wassenaar]

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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