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There are times when it is helpful to have the energy terms actually
added to the System even if that degree of freedom is constrained. Other
parsers (notably the Amber parsers) already support this keyword, so add
that support to ForceField as well

This also replaces some string-based element detection algorithms with
whatever the PDB parser does (by comparing directly to atom.element)

createSystem for both Amber and CHARMM files.

take everything out to a function, RBTorsion and CustomTorsion now use ordering=charmm as their default

Updated description of unit test that was added.

I’m not sure how to trigger the unit testing suite, but this code
should test the changes I’ve made.

This was changed to help debug my development.  I have now returned it
to the original behavior.

This should fix CI build errors in parent repository.

The old _is_gro_coord function inexplicably used split() even though
gro files fixed field (nb: the parsing was still done correctly).  Now
it uses fixed field substrings.

I have made things more technically correct: GROMACS processes pairs
and exclusions separately.  Also added proper support for fudgeLJ term.
Also added improved gro file parsing (technically it’s a fixed-field
format but this works too).

These lines were missed previously

This is the initial commit of my work in getting OpenMM GROMACS support
improved to the point where SMOG SBM simulations run out-of-the-box.
Further commits will be code cleanup.