[gmx-users] elastic restraints in MARTINI simulation

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Mar 23 09:19:06 CET 2016

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).


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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