For questions pertaining to classical force-field methods in computational chemistry, including molecular dynamics simulations using such force fields.

Molecular mechanics uses classical mechanics to model molecular systems. The potential energy is calculated using force fields methods. Molecular mechanics can be used to study small molecules as well as large biological systems or material assemblies with many thousands to millions of atoms.

Some force fields are "all-atom" in which case each individual atom is treated as an individual particle.

Other force fields are "united atom," treating functional groups (e.g., $\ce{CH3}$ or amino acids) as individual particles. Such methods can also be referred as "coarse-grained" methods.