Specifying specific pairwise van der Waals interactions

[Charles Brooks]

Does anyone have experience or examples in how one might specify particular pairs of atoms to interact with specific Lennard-Jones parameters. For example, I would like to specify a "general" non-bonded set of parameters (charge, LJ epsilon and sigma) as the "default" interaction for atoms and then specify that a particular pair (i,j) of atoms use a different epsilon and sigma than that which would be computed from the standard combination rules using the "default" interaction parameters for atom i and atom j. Is this possible with OpenMM functions existing?

[Peter Eastman]

To do this, call addException() on the NonbondedForce. Here is the API documentation for it. Let me know if you have any questions about how to use it.

Peter

[Charles Brooks]

Thanks Peter, think I got it.