[gmx-users] Mdrun and minimum image convention
mark.j.abraham at gmail.com
Wed Apr 15 18:12:23 CEST 2015
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.
> 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.
> 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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