GitLab

* fix to correctly read Gromacs topology files for CHARMM force field

* updated fix to correctly read topology files with NBFIX and different combination rules

* fixes to read topology files with NBFIX and different combination rules

* changed default for useDispersionCorrection to True

* changed docstring default for useDispersionCorrection to 'True'

* fix scaling of 1-4 LJ pairs when NBFIX is used

* apply NBFIXes to 1-4 pairs if no pair parameters are given

* rerun CI

* fix to correctly read Gromacs topology files for CHARMM force field

* updated fix to correctly read topology files with NBFIX and different combination rules

* fixes to read topology files with NBFIX and different combination rules

* changed default for useDispersionCorrection to True

* changed docstring default for useDispersionCorrection to 'True'

* fix scaling of 1-4 LJ pairs when NBFIX is used

* fix to correctly read Gromacs topology files for CHARMM force field

* updated fix to correctly read topology files with NBFIX and different combination rules

* fixes to read topology files with NBFIX and different combination rules

* changed default for useDispersionCorrection to True

* changed docstring default for useDispersionCorrection to 'True'

* Can use getPlatform() instead of getPlatformByName()

* More concise arguments for getState()

* Remove support for Gromacs implicit solvent

* Removed tests of implicit solvent

* 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>

* 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)

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.