[gmx-users] Mdrun and minimum image convention

Catarina A. Carvalheda dos Santos c.a.c.dossantos at dundee.ac.uk
Wed Apr 15 15:54:39 CEST 2015

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.

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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