Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics

Abstract

Coarse-grained (CG) molecular dynamics enables the study of biological processes at temporal and spatial scales that would be intractable at an atomistic resolution. However, accurately learning a CG force field remains a challenge. In this work, we leverage connections between score-based generative models, force fields, and molecular dynamics to learn a CG force field without requiring any force inputs during training. Specifically, we train a diffusion generative model on protein structures from molecular dynamics simulations, and we show that its score function approximates a force field that can directly be used to simulate CG molecular dynamics. While having a vastly simplified training setup compared to previous work, we demonstrate that our approach leads to improved performance across several protein simulations for systems up to 56 amino acids, reproducing the CG equilibrium distribution and preserving the dynamics of all-atom simulations such as protein folding events.