GitLab

All platforms now handle nonbonded exceptions in a consistent way (they ignore cutoffs and periodic boundary conditions).  Also started OpenCL implementation of CustomHbondForce.

Use a consistent (and more accurate) value for electric constant everywhere.  Also cleaned up handling of constants and units in various places.

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.