[siver_john]

Biased: Was a researcher in this field...

For MD, specifically the type talked about here, we aren't taking in all the quantum effects, and that is known. Crystalizing molecules, especially large either dynamic proteins or ones in lipids is hard. Crystalizing during transitory states is orders of magnitude more difficult. MD allows us to visualize those transitory states and was used, for example, to observe the unfolding of the spike protein in Sars-Cov2 to assist in designing mRNA vaccines, because the important amino acids could be observed.

There is a lot of times where it is good enough, outpaces current experimental techniques, etc that it is the tool for the job. But it is not perfect and very rarely can stand completely on its own, in say drug discovery or other fields.