Started work on MCMC using old mcmc.py from yank svn.
More updates on mcmc.py.
Pulled in updated thermodynamics.py, which was overwritten due to an error.
Should match choderalab/repex now
Mostly have finished draft of mcmc.py, but doctests keep segfaulting.  Not sure why.
MCMC doctests pass.  Haven't written them into nosetests yet.
Removed debug code that defaulted to CPU platform.
MCMCSamplerState.createContext() now falls back to CPU and Reference platforms if the specified/default platform throws an Exception on Context creation.
Many more doctests/examples added.
Implemented GHMC moves.  Doctests pass.
Added MC barostat, but not sure if this strategy will work well due to auto move size adjustment.
All MCMC moves (except Langevin) now turn off the barostat to ensure correct function during update().
Fixed a bug with overriding specified timestep in one of the MCMC move types.
Added new "dummy integrator" that doesn't do anything but call the force updates and apply constraints.
Fixed a big problem with random number seeds being reset each time .update() was called.
Added manual test for testing correctness of MCMC.
Modified custom integrator tests to check GHMC.
Updated WaterBox to use simtk.openmm.app.modeller instead of relying upon PDB files.
Corrected errors where new WaterBox code was a method rather than a class.
Added timing instrumentation.  Volume is now stored in the sampler state, as is energies.
MCMC manual test now seems to be working for NPT water box.  Minor fixes to integrators.
Minor fix to statistics reporting for ideal gas.
Added draft of nosetests.
Added 'pymbar' package to setup.py installation requirements.  Added automated testing of potential energies to mcmc nose test.  Removed debug output.
Note that the PyPI version of pymbar will be needed now.
Updated nose test of MCMC to test both volume and potential energy expectations.
Still only test one combination of MCMC moves.