The Multiple Time-Stepping Method for 3-Body Interactions in High Performance Molecular Dynamics Simulations

TL;DR

This paper enhances the efficiency of molecular dynamics simulations involving complex three-body interactions by applying and developing multiple time-stepping and parallelization techniques, including a novel shared-memory approach.

Contribution

It introduces a new shared-memory parallel cutoff method and evaluates multiple time-stepping in the context of high-performance computing for MD simulations.

Findings

Improved efficiency in three-body interaction calculations

Effective parallelization reduces computational costs

Potential for faster molecular dynamics simulations

Abstract

Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on improving the efficiency of MD simulations involving two-body and three-body interactions. Traditional two-body potentials often can not fully capture the complexity of molecular systems, making the inclusion of three-body interactions important. However, these interactions are in a cubic complexity class, compared to a quadratic one for two-body interactions, and therefore are computationally expensive, even when a cutoff distance is applied. One way to improve efficiency is to use the r-RESPA multiple time-stepping algorithm to reduce the number of three-body interaction calculations. In this work, we investigate this method in the context of High Performance Computing (HPC) methods that parallelize the calculations. In particular, we investigate a communication-reducing distributed-memory parallel method from literature and present a novel shared-memory parallel cutoff method, implemented in the particle simulation library AutoPas. The results and methods are discussed, providing insights into potential advancements in MD simulation efficiency.