[gmx-users] Mdrun and minimum image convention

[Mark Abraham]

Hi,

Probably not, unless there's lots of people who'd find it useful. You do
have the option of stopping mdrun periodically and scripting a call to gmx
mindist on the final frame to see if a problem was likely to have occurred
over the trajectory. This would be more efficiently performed during the
simulation (e.g. NAMD lets you call a TCL script you provide, which might
let you implement such a check, but mdrun doesn't have such a feature).
Such a check is rather wasteful (you have to collect coordinates for all
the atoms involved, and then redistribute the work to all the compute
units, then combine the results; or go serial) which makes the benefit (not
wasting simulation time) doubtful given the cost (write a bunch of new code
and add .mdp options for the checking group, the checking frequency and the
distance requirement; run the overall simulation slower).

I'm skeptical it's really useful, though... assuming the problematic case
is something like a protein unfolding, by stopping the simulation and
running it again and hoping it does not unfold so much this time you are no
longer sampling ergodically. If the solute having a large diameter is part
of the expected ensemble, then you need to cater for that in advance.

Mark

On Wed, Apr 15, 2015 at 6:22 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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> Gromacs Users mailing list
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