GitLab

Improved gromacs

Fixes to GromacsTopFile with different combining rules

Defined entry point so other packages can add force field directories

ForceFields can include other files

Fixed bug accessing parameters for CustomHbondForce

Improved logic for guessing elements from atom names

Updated description of unit test that was added.

Added error checking to setNonbondedMethod()

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

Fix typo in bibtex entry

Missing comma causes docs not to compile.

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.

Fix test failure on Jenkins

AMBER-FB15 protein force field parameters

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).