Additional tests

[jesperswillem]

1. Protein system

• protein/water/ligand (Q atoms) system
• eq1 run MD

2. average energy reports in test systems
3. plotting test results

[ChielJespers]

4. Tail of results (--tail). Explanation: only take plot, averages of last results specified by --tail
5. Tee of results (--tee). Explanation: use restart of Q6 having ran --tee steps before doing the new steps

[David-Araripe]

In addition to this, I think it would be helpful to include tests for the Python functions used in the project. Still haven't gotten to it on the branch I'm working on.