On 10/23/19 12:22 PM, Li, Shi wrote:
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
[intermolecular_interactions] are for bonded interactions and [pairs] are for 1-4 interactions.
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?
It sounds like you want to override combination rules, in which case you want [nonbond_params] to create an off-diagonal LJ interaction. A and B need to be defined as different atom types but can have the same LJ so A-A and B-B interactions obey the combination rule but A-B can be whatever you want it to be.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
