[dekhn]

MD was never really a viable way to do structure prediction, so it didn't become obsolete with AlphaFold. Instead, MD is more useful for studying the physical process of protein folding (before the protein folds to its final structure, as well as once it has reached its final structure and sort of jiggles and wiggles around that).

[cowsandmilk]

MD simulations typically aren’t run for time scales that tell you anything about the folding process. Most people are looking at motion after the protein has folded.