Molecular dynamics (MD) is a commonly used method where the Newton's equation of motion
$F_i =- \nabla_i U = m_i\ddot{x_i}$
is solved for every atom $i$ with mass $m_i$, and acceleration $\ddot{x_i}$. The potential energy $U$ describes how the atoms interact, like a Coulomb potential or something.

This is a purely CLASSICAL equation, but it predicts things accurately. For example:
>Pharmacists design drugs by simulating protein atoms interacting with drug atoms.
>Engineers design structural materials by simulating the stretching and bending of molecular systems.
>People routinely simulate molecular systems to calculate heat WHICH AGREES WITH EXPERIMENT!
>Etc.

All using that simple classical equation.

So why does everyone circle jerk over "muh quantum mechanics necessary for small atoms" when clearly these atoms obey Newton's equation of motion?

The world is classical, and classical dynamics determines most interesting things.