[gmx-users] elastic restraints in MARTINI simulation

[Xavier Periole]

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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