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For classroom study - wouldn't straight javascript suffice for basic classical molecular dynamics? That approach would also make it much easier for students to play around with different update algorithms, temperature control, etc.

That would involve

a) writing yourself an engine and that's actual work

b) that engine not being one which is used in real research

So "it depends" – for introductory teaching yes, for training researchers less so.

Teachers can utilize Jupyter notebooks today.

Yep, I will definitively try to compile my Rust MD code to emscripten and give it a look! There are quite a few JS molecules visualizers, so the outcome can be pretty nice for teaching.