In the context of molecular dynamics, when does classical mechanics breakdown? I viewed a lecture and wrote down some of the main points that the professor discussed. One of them was the sufficiency of classical mechanics with respect to molecular dynamics. I’m not well versed on the topic but, the example the professor gave was that Hamiltonian classical mechanics can be used to approximate the potential energy and the kinetic energy of atoms, however when very light atoms are present, such as hydrogen, there are quantum effects, and this can cause errors in molecular dynamics simulations. In the case of hydrogen, with respect to molecular dynamics, does that refer hydrogen as a free atom? If so, does the quantum effect still apply when hydrogen is bonded to another atom? Does the quantum effect exist in molecular dynamics simulations of macromolecules like proteins and cell membranes, because such molecules would have many hydrogen atoms?

Thank you.