[gmx-users] Mdrun and minimum image convention

[Catarina A. Carvalheda dos Santos]

Mark and Tsjerk, thank you both for replying.

I agree that such option would affect the performance and might be a waste
of time, that's why I thought of it as an mdrun flag which can be turned
off by default and turned on if needed. But I understand that adding such
feature is time consuming and that running a mindist to monitor this
(either during or after each "slice" of the trajectory) solves the problem
just fine.

Tsjerk, thank you very much for your help, but I think I got it.

Cheers,


On 15 April 2015 at 21:27, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Catarina,
>
> I have an MD wrapper that comprises a monitoring mechanism, which allows
> terminating a simulation after a certain condition is met. Of course, such
> a mechanism interferes with the MD process, but it will usually add just a
> bit every so many minutes, checking the results at intervals. In a case
> like this, you wouldn't be able to say whether there hasn't been any frame
> with direct interactions, but you can say something about the probability
> it happened. If that sounds good for your purpose, let me know.
>
> To my opinion and experience, having an external monitor works pretty well.
> Trying to include it in the MD code adds clutter there and further burdens
> maintenance. And doing such calculations at every frame also adds a
> significant cost.
>
> Cheers,
>
> Tsjerk
> On Apr 15, 2015 6:23 PM, "Catarina A. Carvalheda dos Santos" <
> c.a.c.dossantos at dundee.ac.uk> wrote:
>
> > Thank you for the clarification Mark.
> >
> > Would you consider to add such feature (as an mdrun flag for example: -pi
> > <index_group>) in the next GROMACS versions?
> >
> > On 15 April 2015 at 17:12, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >
> > > Hi,
> > > On 15/04/2015 3:55 pm, "Catarina A. Carvalheda dos Santos" <
> > > c.a.c.dossantos at dundee.ac.uk> wrote:
> > > >
> > > > Hi there,
> > > >
> > > > Is there any way to control the minimum distance with periodic images
> > > > during mdrun and exit the simulation automatically if this distance
> is
> > > > equal or lower than the user-defined cutoff? I know that this can be
> > > > monitored with g_mindist, but doing it automatically would avoid
> > wasting
> > > > simulation time.
> > >
> > > No there's no way to do that - mdrun has not been told what part of
> your
> > > simulation is special. By the way, the minimum image convention is a
> > > different thing, related to whether particles can see only one image of
> > > each other particle within the short-ranged cut-off. This is enforced.
> > But
> > > whether a whole solute can see more than one image of itself is not.
> > >
> > > Mark
> > >
> > > > I was told that Amber and NAMD simulations crash when the minimum
> image
> > > > convention criteria is not met, but the same doesn't happen with
> > GROMACS
> > > > runs which keep running without even a warning message (at least I
> > can't
> > > > find any in my log files).
> > > >
> > > > Am I missing something here?
> > > >
> > > >
> > > > Thank you for your time.
> > > >
> > > > Regards,
> > > >
> > > > --
> > > > Catarina A. Carvalheda
> > > >
> > > > PhD Student
> > > > Computational Biophysics Group
> > > >
> > > > Centre for Translational & Interdisciplinary Research
> > > > University of Dundee
> > > > DD1 5EH, Dundee, Scotland, UK
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> > --
> > Catarina A. Carvalheda
> >
> > PhD Student
> > Computational Biophysics Group
> >
> > Centre for Translational & Interdisciplinary Research
> > University of Dundee
> > DD1 5EH, Dundee, Scotland, UK
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-- 
Catarina A. Carvalheda

PhD Student
Computational Biophysics Group

Centre for Translational & Interdisciplinary Research
University of Dundee
DD1 5EH, Dundee, Scotland, UK