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

[Justin Lemkul]

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

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================