[infinite8s]

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.

[genericpseudo]

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.