GitLab

Commented out some minor optimizations in AMOEBA that were making the forces incorrect.  AMOEBA energies and forces now agree with TINKER to within 1e-9 (fractional energy) 1e-5 (fractional RMS force error) for NPT simulations on rectangular water boxes with PME and direct or mutual polarizability.

CustomNonbondedForce.cpp, CudaNonbondedUtilities.cpp and CudaKernels.cpp are now fully reverted to 3478.

LPW attempted bugfixes: (1) Changed unit multipliers in AmoebaVdwForce::getParticleParameters (2) Sorted vectors in exclusionLists so it agrees with atomExclusions