[gmx-users] elastic restraints in MARTINI simulation

[James Starlight]

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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