Molecular Dynamics Simulations Accelerated on FPGA with High-Bandwidth Memory

Abstract

Molecular dynamics (MD) simulation is a powerful tool for investigating complex systems in physical, materials, and biological sciences. However, computational speed remains a critical bottleneck that limits its broader application. To address this challenge, we developed a dedicated hardware module based on modern field-programmable gate arrays (FPGAs) that accelerates all components of MD simulations. Our design employs pipelining strategies to optimize task execution within a fully parallel architecture, significantly enhancing performance. The latest generation of high-bandwidth memory (HBM2) is integrated and optimized to improve computational throughput. At the hardware level, we implemented an optimized register-transfer level (RTL) circuit design for a single node to maximize the efficiency of register read and write operations. Software co-design with SIMD frameworks ensures seamless integration of force calculations and system propagation. We validated the implementation across systems ranging from argon gas to solvated proteins, demonstrating stable MD trajectories and close agreement with reference energy values. This work presents a novel FPGA-based MD simulation architecture and provides a foundation for further improvements in hardware-accelerated molecular simulations.