On Fri, Mar 15, 2013 at 7:27 PM, Jeff Woodford < jwoodf...@missouriwestern.edu> wrote:
> Hi all, > I am attempting to simulate a system that has strong ionic character so I > would like to treat the electrostatics and van der Waals interactions > separately. For example I would like to include all pairs of atoms in the > electrostatics calculation but I would like to exclude 1-2 and 1-3 > neighbors in the van der Waals calculation. Is this possible to do in > GROMACS? If so, how might this be accomplished? Thanks in advance for > your help. > Should be possible, but I don't think it's something for which GROMACS explicitly caters. I'd suggest keeping the normal exclusions for the [moleculetype] (e.g. nrexcl=3). For each 1-2 and 1-3 interaction, add [pairs] interactions that have zero VDW parameters. See manual 5.3.4, and other bits of chapter 5. You may be able to hijack the [pairtypes] mechanism here, depending whether the [pairs] mechanism is already being used by your force field for 1-4 interactions. Otherwise, I think something like [pairs] ; i j functype c6 c12 1 3 1 0 0 is the right kind of way to put a no-LJ normal-Coulomb interaction between atoms 1 and 3. Not sure offhand how to scale down the charges (which you'd probably want). You'd have to generate that list of 1-2 and 1-3 pairs yourself, but you can probably hijack the contents of the [bonds] and [angles] fields to save some legwork. Mark -- 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
