[gmx-users] elastic restraints in MARTINI simulation

[Mark Abraham]

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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