Graph neural network force field computational algorithms for molecular dynamics computer simulations

Abstract

A computational method simulating the motion of elements within a multi-element system using a graph neural network (GNN). The method includes converting a molecular dynamics snapshot of the elements into a directed graph comprised of nodes and edges. The method further includes the step of initially embedding the nodes and the edges to obtain initially embedded nodes and edges. The method also includes updating the initially embedded nodes and edges by passing a first message from a first edge to a first node using a first message function and passing a second message from the first node to the first edge using a second message function to obtain updated embedded nodes and edges, and predicting a force vector for one or more elements based on the updated embedded edges and a unit vector pointing from the first node to a second node or the second node to the first node.