Ehm, what? I know what you are saying, but just because you need some kind of interaction to measure ANYTHING. Or in other words with that logic you couldnt even measure the impuls of a flying particle because to measure it, the particle would need to interact with another particle somehow. In a simulation you for example could measure the energy level of a single particle and then determine its state. So here for md. For dft simulations you could also use the electron probability densities to determine the distance to other particles.

This kind of access to the physics are not availible for a single atom ofc