RBMD: A molecular dynamics package enabling to simulate 10 million all-atom particles in a single graphics processing unit

TL;DR

This paper presents RBMD, a GPU-accelerated molecular dynamics package capable of simulating up to 10 million all-atom particles efficiently using random batch methods for nonbonded interactions, surpassing traditional methods in speed and scalability.

Contribution

The paper introduces a novel GPU-based molecular dynamics package that employs random batch algorithms for nonbonded interactions, achieving linear complexity and enabling large-scale simulations on a single GPU.

Findings

RBMD achieves linear complexity in Coulomb interaction calculations.

It can simulate up to 10 million particles on a single GPU.

RBMD outperforms traditional methods like P3M and Verlet lists in efficiency.

Abstract

This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of particle systems. The long-range part of Coulomb interactions is calculated in Fourier space by the random batch Ewald algorithm, which achieves linear complexity and superscalability, surpassing classical lattice-based Ewald methods. For the short-range part, the random batch list algorithm is used to construct neighbor lists, significantly reducing both computational and memory costs. The RBMD is implemented on GPU-CPU heterogeneous architectures, with classical force fields for all-atom systems. Benchmark systems are used to validate accuracy and performance of the package. Comparison with the particle-particle particle-mesh method and the Verlet list method in the LAMMPS package is performed on three different NVIDIA GPUs, demonstrating high efficiency of the RBMD on heterogeneous architectures. Our results also show that the RBMD enables simulations on a single GPU with a CPU core up to 10 million particles. Typically, for systems of one million particles, the RBMD allows simulating all-atom systems with a high efficiency of 8.20 ms per step, demonstrating the attractive feature for running large-scale simulations of practical applications on a desktop machine.