> > > Den 2019-10-23 kl. 18:22, skrev Li, Shi: > > Dear GMX users, > > > > I am wondering if there is a way to define the intermolecular interaction > > to simulation a binary LJ system. For example, I have two atoms A and B, > > they share the same LJ parameter, and I want to change the interaction > > parameter between A and B, so that I would expect different behaviors > from > > the simulation (mix or phase separation). > > > > I checked the manual and found this can be defined in the topology file > as > > [intermolecular_interactions] and use the [pairs] interaction then list > the > > atom pairs. But it is still confusing if I have a system containing 500 A > > and 500 B, how can I apply this to the entire binary system. I was > > assumed that I can use atomtype instead of atom number? But how and where > > to specify that? > > > > Any suggestions? > > > > Thanks, > > Shi > > > Use > [ nonbonded_types ] > A A 1 c6 c12 > B B 1 c6 c12 > A B 1 c6 c12 > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > > > Thank you so much! This works very well.
Shi > > -- 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.