Implicit solvent approach based on generalized Born and transferable graph neural networks for molecular dynamics simulations.

Abstract

Molecular dynamics simulations enable the study of the motion of small and large (bio)molecules and the estimation of their conformational ensembles. The description of the environment (solvent) has, therefore, a large impact. Implicit solvent representations are efficient but, in many cases, not accurate enough (especially for polar solvents, such as water). More accurate but also computationally more expensive is the explicit treatment of the solvent molecules. Recently, machine learning has been proposed to bridge the gap and simulate, in an implicit manner, explicit solvation effects. However, the current approaches rely on prior knowledge of the entire conformational space, limiting their application in practice. Here, we introduce a graph neural network based implicit solvent that is capable of describing explicit solvent effects for peptides with different compositions than those contained in the training set.