Added TODO list.

TODO.md

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+# 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?