Updating Files from Parent Repo#1
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Make various updates to MD/MC lectures
Slightly cleanup 3D structure/shape assignment to standardize with lecture
Update library searching lecture/sandbox slightly
Slightly update ligand based design slides
Make clarity/usability improvements to a couple notebooks
Correct keynote slides for a couple lectures
Update error analysis/convergence examples
Update visualization notebook
Update some content for 2025
Include some updates to MD assignment and README.md
Make additional updates for 2025 to 3D strucutre/shape and MC
…put-only rather than inout; caused problems on some platforms.
Fix a couple issues, one critical to MD assignment on Colab
Correct prior error introduced in mdlib
Update physical properties slides and notebooks
Update library searching asssignment to make more clear they should submit code
Update error analysis code for 2025 OpenFF and OpenMM
Update proteins lecture for 2025
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