Feedback from MolSim 2021

[dwhswenson]

A few points that came up in discussions, mostly with the TAs, from MolSim 2021 as to ways to improve the tutorial. The main theme is that there are a lot of places where the student is to answer some question, but no context is provided for why that question is something you might want to look at.

For all notebooks:

• Make sure that axes are labelled in plots
• Possibly recommend installing requirements via the conda env used by binder [EDIT: This was because, at the time, OpenMM didn't work on Python 3.8 or 3.9. Now that OpenMM is on conda-forge, this is not a problem.]

From notebook 2:

• What is the significance of getting both forward and backward paths?
• Why do we care about number of steps between decorrelated trajectories?
• Why might you visualize the shooting points?
• Better explain significance of fixed-length vs. flexible-length TPS
• Maybe clarify that there are many paths that switch channels (in the path density)
• Fix grammar on last sentence of the notebook

From notebook 3:

• Clarify the need for full equivalence, i.e., must show that both q=q* => p_B(q)=1/2 and p_B(q)=1/2 => q=q*.