GitLab

* Remove support for Gromacs implicit solvent

* Removed tests of implicit solvent

* Replace distutils with setuptools

* Replace more uses of distutils

* Support GROMOS bond and angle types

* Support NBFIX with geometric combining rule

* Continuing GROMOS support

* Bug fixes

* Fixes to test case

* Update wrappers/python/openmm/app/gromacstopfile.py
Co-authored-by: Jason Swails <jason@entos.ai>

* Improve logic for handling dihedraltypes

---------
Co-authored-by: Jason Swails <jason@entos.ai>

* Avoid adding duplicate exclusions to CustomNonbondedForce

* Fixed error in adding explicit constraints

* Top level Python module is now "openmm"

* Updated module names in examples

* Updated module names in documentation

* Updated module in CI scripts

* Added deprecation warning

* Do not alter mass of hydrogens in rigid water

* Do not alter mass of hydrogens in rigid water

- Test system is translated to the origin
- Energy is computed again after updating Gromacs input to reflect no-cutoff option (rcoulomb = rlist = rvdw = 0.0)

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

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.

Swigged python docstrings now include documented return values and type
information or their arguments. They are generated in numpydoc format.
Furthermore, all of the Python app layer docstrings have been changed
to numpydoc format. The filterPythonFiles.py script which helps to
generate the Doxygen Python API docs has been updated to reflect these
changes.

This was actually fully supported already, since it parsed pairtypes and
assigned the exception parameters correctly from there. All this does is throw
an exception when pair parameters are not defined and gen-pairs=no.

Virtual sites are never created by the OpenMM system, and their information is
not parsed from the Gromacs topology file. For now just throw an exception
rather than let them run, since TIP4Pew behaves *very* strangely...

Gromacs uses the preprocessor to replace previously #define'd tokens in strings.
This is used, for instance, to override certain parameters without having to
introduce new file types.  This is how Gromacs implemented ff99SB-ILDN (i.e., by
simply replacing the chi torsion for isoleucine, leucine, aspartate, and
asparagine with a define token).  So OpenMM *was* missing some in-line
parameters that were defined.

The immediate consequence I see is that whenever someone tried to run
ff99SB-ILDN with OpenMM, what they were *really* getting was ff99SB. Not sure
where else, if anywhere, this kind of thing was happening.