[gmx-users] elastic restraints in MARTINI simulation

[Tsjerk Wassenaar]

Hmm, the first one ends the abstract with

"Correct dynamical properties, at least those studied in this paper, are
obtained with the Berendsen thermostat applied globally, despite the fact
that it yields the wrong kinetic energy distribution."

So what does (un)physical mean in this respect, in relation to Berendsen,
Langevin, and other coupling methods? Is giving the wrong dynamical
properties (like Langevin) still physical? Or is a correct distribution of
kinetic energy more physical than failing on dynamical properties?

Cheers,

Tsjerk
On Mar 23, 2016 12:13, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:

> 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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