Maybe a stupid question, but isn't it require to run these long-time simulations multiple times anyways? So one could evaluate these all at once by introducing

Maybe a stupid question, but isn't it require to run these long-time simulations multiple times anyways? So one could evaluate these all at once by introducing randomness (vibrations, small rotations, dihedral angle changes, etc) once an interesting point in time is reached, and then simulating in parallel from then onward.