If you want to get pedantic we can't simulate anything with complete accuracy in the absence of a theory that encompasses all the known forces. Which we don't have. (Damn you gravity. Can't you just get along with the others)

To a useful level of accuracy we can certainly simulate water. And we can do the same for a single proton for some definitions of useful (but not other definitions).

That's a fundamentally different problem and a terribly unfair comparison.