Justin A. Lemkul wrote > > > You don't need the pull code if the two atoms are in the same > [moleculetype] - a > "molecule" in Gromacs is any set of atoms; they don't necessarily have to > make > chemical sense. The only problem I see is that if you have two atoms in > the > same location, while simultaneously turning one "on" and the other "off," > you > will likely develop strong repulsive interactions between them such that > the > constraints may fail and your atoms will be displaced from the desired > location. > I can't say for sure whether it will be a problem, but if you've got > atom A > existing at 20% and atom B trying to exist at 80% in the exact same > location, > that sounds like a recipe for trouble. > >
OK, thanks very much for the advice, however, I'm not following something here- maybe I am just being dense: I thought the point was that the Fe2+ and Fe3+ ions cannot be in the same molecule, because the lookup tables for their short ranged interactions need to be assigned using energygrps, which seem to apply to molecules not atom types. If the tables could be applied to atom types rather than molecules (which makes more sense to me anyway), then there would be no problems. I thought it was possible in GMX to completely switch off all interactions (including coulomb and vdw) between selected molecules. If so, then when one "turns on" while the other "turns off" they never interact, correct? Maybe I am wrong that it is possible to exclude all interactions between two given molecules? -- View this message in context: http://gromacs.5086.n6.nabble.com/BAR-calculations-with-tabulated-non-bonded-potentials-tp4993395p4994907.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists