GitLab

simulateCharmm.py to use the latest force fields. This is what CHARMM does for
their own tutorials, so this is fine.

to prevent users from actually using them.

ERROR: Test that altering the mass of hydrogens works correctly.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/SimTk/openmm/python/tests/TestCharmmFiles.py", line 91, in test_HydrogenMass
    topology = self.psf_v.topology
  File "/usr/local/lib/python2.7/dist-packages/simtk/openmm/app/charmmpsffile.py", line 777, in topology
    masselem = Element.getByMass(mass)
NameError: global name 'Element' is not defined

pickleability.

- Add a docstring to element.Element.getByMass describing what it does
- Add a new element virtualsite with atomic number 0 (and alias it to extrapoint
  and lonepair)

Include force groups when serializing forces

Cleanup to the recent serialization code changes

constructor _should_ be able to take all of files in the CHARMM parameter set
distribution and correctly determine file type from just the name and/or
filename extension.

Added missing serialization support for CustomNonbondedForce group interactions

Added defaults to make serialization of CustomNonbondedForce and NonbondedForce backward-compatible.

parameters to a ProteinStructure before calling createSystem.

Updated tests of serialization of CustomNonbondedForce, though test omits comparison of interaction group sets since I couldn't figure out how to do that.