Hi, 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.
Mark On Tue, Feb 28, 2017 at 10:22 AM <p...@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 > 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. > -- 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.
