feature_gromacs_energy

[chryswoods]

This feature branch contains the code developed to support calculating internal energies of molecules parameterised to include Gromacs-style dihedrals (e.g. specifically the harmonic improper term). This will also include adding support to the OpenMM converter for writing Urey-Bradley angle terms and harmonic improper terms.

API Proposal

This should be fully automatic and require no changes to the API. Essentially molecules that contain such internal terms will now not trigger exceptions saying that only amber-style dihedrals are supported.

>>> mols = sr.load("files_containing_gromacs_dihedrals")
>>> mols.energy()
Result!
>>> mols = mols.dynamics().run(5*sr.units.picosecond).commit()
Result!

[chryswoods]

I'm archiving this as I haven't had a chance to look at it. It can be revived later if there is interest.