Yes, that's my point: you don't need to simulate a protein with that tool because we have good enough models of higher level structures like atoms. And similarly we might find models for neurons that allow us to avoid full emulation all protein interactions. We figured out how atoms work before we figured out how nuclei work, but with neurons it's the opposite: we know/can figure out how the the parts (proteins) of the machine work but not how the entire machine works.