Add (optional) topology to testSystems

[jhprinz]

This would come in very handy for our purposes. If at least in some systems we could get an openmm.Topology() object or mdtraj.Topology() object that would be great. Maybe we can add an extended TestSystem like

class ExtendedTestSystem(TestSystem):

    def __init__(self, args, topology):
        super(ExtendedTestSystem, self).__init__(args)
        self.topology = topology

This might make it easier to analyze results later. Any ideas?

Mention @dwhswenson here to get his opinion.

[kyleabeauchamp]

See #8

Also, we should probably not impose an MDTraj requirement here, so it will have to be an openmm topology for now. It's easy enough to convert to MDTraj from OpenMM...

[kyleabeauchamp]

Actually, I suppose we could also expose an MDTraj topology if we keep use local imports to avoid a install-time dependency.

[jhprinz]

openmm.Topology is fine. mdtraj can convert easily enough. If there is no objection I would add the topology to some of the examples that I use. We can see if that makes sense.

[jchodera]

Let's use the OpenMM Topology for this.