Merge pull request #2 from swails/master

Added CustomGBForce implementations from Jason Swails that allow deactivated protons to be omitted from GB calculation.
Modified cpin.  Now generated via Python cpinutil, which will be supported going forward (over Perl version).
Added MBAR reference.
Updated README.
Updated README.
Added workaround for issue with OpenMM where changing number of exclusions (exceptions with zero energies) in CustomNonbondedForce via updateParametersInContext would cause an error.
Ugly hack sets these parameters to machine precision instead of zero.