TODO list for alchemical tools

`alchemy.py`

Code cleanup

Replace ONE_4PI_EPS0 with import from simtk.openmm.constants once OpenMM internal constants are available there

Alchemical protocol specification

Allow alchemical protocols to be specified by YAML files (for YANK)
Eliminate default alchemical protocols in code and replace them with a library of YAML files for different kinds of protocols

Tests

Add tests for alchemically softening loops (for loop model refinement) and proteins (for model refinement) using no-cutoff methods
Add thorough tests for overlap with original (unmodified) states
Test to make sure energies are never NaN

Forcefield support

PME

Can we get around the neglect of reciprocal-space components of electrostatics?

Implicit solvent models

Make support for implicit solvent models generic by rewriting force terms in a general way

AMOEBA

Finish support for AMOEBA

Other electrstatics models

Add support for Wolf-like electrostatics?