That depends on the granularity of your simulation. For most - not all - purposes a glass of water can be simulated coarsely or by simulating a far smaller amount with greater fidelity and then to extrapolate.
For useful materials science the numbers are still large but far lower than the numbers involved in 'a glass of water'.
I really depends on what is needed. If you know that something quite "coarse" is enough to create/uncover room temperature superconductors with high critical current - fair enough. Again, we'll see what happens.