[gmx-users] Simulation crashes: issue with [pair] potential

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 28 17:03:49 CET 2017


Tabulated non-bonded potentials are possible (see manual), but currently
only implemented between pairs of energy groups, and only in the group
cut-off scheme. So by e.g. putting each type of particle in its own energy
group you can arrange for whatever inter-group interactions suit you. But
there's only a small number of groups possible, maybe 64 or 128? I forget.


On Tue, Feb 28, 2017 at 10:22 AM <poma at ifpan.edu.pl> wrote:

> Hi,
> We had employed the pair potentials in unconventional way.  They were used
> to describe nonbonded specific Lennard Jones (LJ) Potential between a pair
> of particles. Each pair has a different set of sigma's parameters, but
> just one epsilon. Although they are LJ potentials, they are considered as
> bonded interactions by definition and a table is made internally. When
> bonded interactions exceed the minimum convention image distance (MCID),
> then the simulation generally crashes due to a distance which is above the
> Obviously, Gromacs starts complaining about this issue with a warning
> regarding a distance between two atoms which is reasonably large and it
> assumes that we are performing a free energy calculation. Has anybody
> encounter a similar issue before, honestly I would like to find another
> way to define the interaction between pair of particles as purely
> nonbonded potential (with different sigma's parameters) and not as pairs,
> any help will be appreciate!
> kind regards,
> --
> Dr. Adolfo Poma
> Institute of Physics
> Polish Academy of Science
> Al. Lotnikow 32/48,
> 02-668 Warsaw, Poland
> --
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