First draft of the trajectory_example code.
Roughly working version of trajectory_example.

Now the point is to clean this up until it works smoothly.
Solvect/Solvent.... I've heard it both ways.
Reports Ramachandran angles.
trajectory_example now contains state/iface defs.

Also switched to amber96 to be consistent with JDC and PGB's earlier papers
on Ala-dipeptide.
LambdaVolumePeriodic and working tests.
Correction to atoms labelled as psi atoms.

Doesn't change any behavior, just fixes typos. Turns out PDB counts from 1,
we count from 0.
Progress on the example; mainly commit-as-stash.
Merge branch 'enter_exit_ensembles' into example_traj

So I can use my EntersXEnsemble and ExitsXEnsemble classes on the example
script I'm assembling.
Commit-as-stash to make SequentialEnsembles.
Merge remote-tracking branch 'upstream/master' into example_traj
Renamed trajectory_example->ala_dipeptide_example

Also started including SequentialEnsemble for first trajectory in that.
Merge branch 'sequential_ensemble' into example_traj
Merge branch 'lambdavolumeperiodic' into example_traj

Conflicts:
	code/python/PySRMSTIS/src/tests/testvolume.py

Also includes fixes to ala_dipeptide_example to get it working with new
storage.
Example generates the first TIS path! Woohoo!
Merge remote-tracking branch 'upstream/master' into example_traj
One small fix to play nicely with new storage.

Problem was my foolishness anyway.
Merge pull request #38 from dwhswenson/example_traj

Alanine Dipeptide Example Traj