GitLab

Redesigned CustomNonbondedForce to eliminate combining rules and allow the expression to directly use parameters for individual particles.

Free energy plugin added
Plugin will not run w/ Obc or GB/VI forces unless line 2004 of gpu.cpp (gpu->sim.totalNonbondOutputBuffers  = 2*gpu->sim.nonbondOutputBuffers;) is commented in -- working on removing this constraint
Also unit tests for GB/VI currently fail 

Restructured how force and energy computations are done to make it easier to write plugins for the CUDA platform

All energies existing in Preview Release 3 now run on the GPU, new Ewald energy terms still use Reference implementation

In calcForces() kReduceBornSumAndForces kernel is not needed since Born radii/Obc chain term now calculated prior to calculation of forces
Modified kCalculateObcGbsaBornSum kernel loop to match that in kCalculateCDLJObcGbsaForces1; Born sums are zero w/o mods