[gmx-users] elastic restraints in MARTINI simulation

[James Starlight]

OK, I will try now!
May the error be related to big shift of the receptor within thw
membrane plane due to the tranlational diffusion7
I made vizualization of the trajectory in VMD and observed relatively
big motion of the protein within membrane plane due to the tendency of
the oligomerization of several subunits.

2016-03-23 9:37 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
> 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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