Merge pull request #46 from jhprinz/master

Updated showtree.py
create store for orderparameters
more cleanup for op storage
Implemented PathReversal and ReplicaExchangeMove
Added GlobalState class
Fixed more on OrderParameter storage
Initial draft of OpenMMSimulation interface obj.

The idea is that we add an interface to separate the details of the
implementation of structures in the MD engine from the things we really need
to get back from the MD engine. This gives a taste of how to do that; still
need to change the core files so that they support this (mainly snapshot and
simulator)
Replaced OpenMM Simulation with our subclass.

Seems to run the alanine example without trouble (although JHP's switch to
frames every 2ps means I wait a lot longer for a new frame!)
Support for stop() function.

Not used in OpenMM (or my planned toy MD), but might be useful for Gromacs
or other external tools.
Changed snapshot behaviour to be stored separately
Correction for calling the stop function.
Merge pull request #48 from dwhswenson/decouple_dynamics

Decouple dynamics engine
fixed errors in storage simplification
Merge branch 'master' of github.com:choderalab/msm-tis into snapshotchange

Conflicts:
	opentis/snapshot.py
Fixed sandbox and Simulator to run with new OpenMM Simulator object
Fixed showtree.py for new storage
Fixed showtree.py plot range
minor improvesments on globalstate