Update Session 2 - MD of a LJ system

[summeraz]

Session 2 will introduce the students to what an MD simulation script looks like (we will be using HOOMD) and will have them perform some simulations of a simple LJ system in various ensembles. We may only use a single Jupyter notebook for this lesson (although it might be beneficial to break this up into multiple notebooks in case students "break" their initial notebook - maybe we should have a backup of all notebooks somewhere on the VM).

• Walk through a simulation script line-by-line explaining (with visuals - within the notebook - where applicable) each line/section
• Introduction to neighborlists
  • These are not touched on in any of the lectures, so we can touch on them here.
• Performing simulations of LJ systems in NVT and NPT ensembles
  • View trajectories in the notebook using NGLview
  • Plot various quantities (temperature, energy), use block averaging