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

poma at ifpan.edu.pl poma at ifpan.edu.pl
Tue Feb 28 10:22:40 CET 2017

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

More information about the gromacs.org_gmx-users mailing list