[gmx-users] elastic restraints in MARTINI simulation

Wed Mar 23 13:42:09 CET 2016

1) I guess Langevins used as thermostat works good as some kind of
imitation of thermal motion produced by collisions of atoms with
virtual particles in case when we modify tau_t depending of what kind
of system we simulate e,g protein in water or in membrane. Why such
algorithm produce wrong dynamical properties

2) I also been surpriced why in a lot of recent papers focused on GPCR
modeling people used Berendsen tcoupling method instead of Nose'Hover
or V-rescale for instance.

J.

2016-03-23 13:15 GMT+01:00 Tsjerk Wassenaar <tsjerkw at gmail.com>:
> 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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