Update (and expand) notebooks for lectures

[davidlmobley]

The notebooks and worked examples for lectures need updating, particularly, these cases:

• Python, Linux, and vi(m)
• 3D structure and shape methods (Modernize 3D structure/shape notebook and supporting materials #25 )
• Molecular dynamics (MD) -- currently I only have a "sandbox" for use in class and lecture material is still just slides
• Monte Carlo (MC) -- currently I have a "sandbox" for use in class and lecture material is still just slides
• Library searching -- currently I have a sandbox; rest of material is still just slides.
• Ligand-based design -- currently I have a sandbox; the rest of the material is still just slides.
• Physical property estimation
• Docking; slides have most of the material
• OpenMM, MDTraj, clustering and visualization: Probably should be updated/extended to use examples from @nathanmlim 's work on BLUES
• Mixture simulations

(I have a separate issue for the lectures which do not yet have any notebooks, #4 ).