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

[David van der Spoel]

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