Support for non-standard mixing rules

[cwalker7]

We want to be able to use mixing rules other than the standard Lorentz-Bethelot, to investigate things like weakening the sidechain-backbone interaction strength while keeping the other interaction strengths constant.

It looks like binary interaction parameters or custom mixing rules are not supported with the standard openmm.nonbondedforce - the Lorentz Berthelot is always used. http://docs.openmm.org/latest/api-python/generated/simtk.openmm.openmm.NonbondedForce.html

Seems like there are a few different ways of going about this:

1. Use a customNonbondedForce and add a binary interaction parameter to the epsilon mixing rule (eps_ij = (1-kappa)*sqrt(eps_ii*eps_jj) http://docs.openmm.org/7.1.0/api-python/generated/simtk.openmm.openmm.CustomNonbondedForce.html
2. Define interactions groups such that we can specify different parameters for like particles and unlike particles. For example, making epsilon of sidechain beads lower for unlike interaction group and higher for like interaction group will result in comparatively weaker backbone-sidechain interactions, even though the Lorentz-Bethelot rule is still applied.