[gmx-users] elastic restraints in MARTINI simulation

[Mark Abraham]

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 <x.periole at rug.nl> 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 <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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