[gmx-users] Mdrun and minimum image convention

[Tsjerk Wassenaar]

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
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> > The University of Dundee is a registered Scottish Charity, No: SC015096
> >
>
>
>
> --
> Catarina A. Carvalheda
>
> PhD Student
> Computational Biophysics Group
>
> Centre for Translational & Interdisciplinary Research
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>