Create Jupyter notebooks with content (and, ideally, activities) for missing lectures #4
Description
Currently, I do not have Jupyter notebooks for the following lectures, so I will need to create them (potentially from the slides), ideally also creating activities to try at the same time.
- Energy minimization
- [ ] Quantum mechanics - Solvation models (should probably update to have example OpenMM code using GBSA solvation, computing solvation free energy with radius updates)
- Fluctuations, correlations, and error analysis (use density example and other samples from OpenMM).
- Error analysis, part 2
- Working with proteins (whole content for this one needs replacing, not just migration from slide format, probably to use OEBio)
- Molecular visualization (needs updating to NOT exclusively use PyMol but also provide VMD intro)
- Normal modes
- Free energy calculations and the drug discovery process
Add content to solvation lecture on explicit solvent.
Please let me know if you're interested in helping with/taking ownership of content for any of these, especially if it overlaps with something you are already working on. I have slide content I could share and we could talk through what the material should cover. (cc @nathanmlim @sukanyasasmal @vtlim @bergazin )