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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?

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

Thanks Peter, think I got it.