GitLab

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

pick up some bugs that were not caught in my initial test following the port
from ParmEd.

All 4 tests pass right now, although no periodic systems are being tested.
Currently CHARMM, XPLOR, and VMD tests are all being run (for the same ala-3
system).

Disable implicit solvent tests, since there is no robust radii assignment
routine yet (the radii are stored in the Amber topology file).  I will port my
assignment routine from ParmEd here shortly and then re-enable the GB tests.

Add a test case and example for running with CHARMM files.