Reorganized some files.
Updated files to set up example YANK calculation.
Updated setup script.  Seems to run now!
Major changes to p-xylene example.
Removed --ignore_signal option, since this was just an SGE workaround hack.
Updating p-xylene example.
Added workaround for bug where segfault would be caused if all atoms in system were added to alchemical region.
This caused a problem with group restrictions of CustomNonbondedForce segfaulting if any atomset is empty.
Converted from old Set usage to built-in sets.
Fixed nasty bug that was causing test_alchemy to fail on LennardJonesFluid.
Added a draft README to benzene-toluene.
Fixed double-inclusion of driver code in yank.py.
Minor tweaks to restore normal functioning for p-xylene example on GPU cluster.
More minor fixes to serial execution code path.
Generalized restraints.py classes.
Fixed a bug in the radius of gyration computation.
Updated resuming code for serial codepath.
Removed the rest of the old scheme where solvent and complex simulations could be run in parallel to make code maintenance simpler.
Many bugfixes to get MPI working.
A few more bugfixes for MPI and CUDA.
Updated analyze.py to analyze results of a single simulation.
Added Torque/Moab batch queue example script.
Minor bug fix to harmonic restraint usage.