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 

Comparison of the forces in the Ewald/PME reference tests is disabled by default. If set, they are compared to the double precision output from Gromacs.

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

The differences in the Ewald energies between the Reference and Cuda platforms were traced to roundoff error in the 
computation of the Vdw and Coulomb ixns for the short-range energy contribution (verified using double precision in the sum); the vdw and Coulomb terms are now accumulated separately and then added to the total energy 

In Ewald SR portion of code, the LJ contribution to dEdR was missing a factor of (inverseR*inverseR)