add examples / testcases

[Marcello-Sega]

Feel free to add to this list:

• [x] document group.clusters and group.sides (Marcello)
• [ ] add scaling of other algorithms (Marcello)
• [ ] make a more visible example (manual, notebooks, examples) on how to use a trajectory (Gyorgy)
• [ ] add example on how to use DBSCAN (examples) (Gyorgy)
• [ ] test that all examples work (Gyorgy)
• [ ] add example on how to use the extra groups for mixed interfaces (manual, examples, notebooks)
• [ ] add LAMMPS example/testcase (dcd trajectory ?; Marcello, Gyorgy)
• [ ] add NAMD example (Marcello)
• [ ] add an example (with capital letters warning) in the manual on how to load beta factors in multiple frames pdb file (Marcello)
• [ ] document and describe the MonteCarlo normalization (Marcello)
• [ ] Tutorial on Multiple interfaces (layers of CCL4 as seen from interface of water) (Gyorgy)
• [ ] Check that all observables are documented/described
• [ ] Correlation function (variable groups) expand documentation and add Tutorial (Balazs)
• [ ] Add trajectory handling (+discussion of the mechanism) in quicktour (Gyorgy)
• [ ] Add Tutorial about trajectory handling (in detail, including manual procedure) (Gyorgy )
• [ ] Check numbers in micelle tutorial (Marcello)
• [ ] Check centering (Marcello, Gyorgy)
• [x] mdtraj integration: add an example to the manual
• [x] related to mdtraj: add an example about how to interact with openMM
• [x] replace the image in README.md with markdown