[gmx-users] Define intermolecular interactions in L-J simulation

[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