[gmx-users] Mdrun and minimum image convention

[Catarina A. Carvalheda dos Santos]

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