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 MCID. 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 -- 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-requ...@gromacs.org.
