We can use coarse-grained molecular dynamics (CGMD) models, namely, the “bottom-up” force-matching- and “top-down” free energy-based approaches to describe biological complex system.

A complete coarse-grained model must include two components: a mapping from atomistic structures to coarse-grained (CG) “beads” and a set of potentials that describe the interactions between beads.

The former defines the geometry or length scale of the resulting model, while the latter defines the “force field”. The parameterization of the force field is essential to the performance of the model, which is only relevant insofar as it can reproduce experimental observables.

Recent improvements to widely-disseminated force fields have strengthened both their transferability the ability to use a model on novel biophysical system with straightforward parameterization as well as tunability, the ability to customize a model to match a desired quantity.