FPGA Accelerators for Computing Interatomic Potential-Based Molecular Dynamics Simulation for Gold Nanoparticles: Exploring Different Communication Protocols

Abstract

Molecular Dynamics (MD) simulation for computing Interatomic Potential (IAP) is a very important High-Performance Computing (HPC) application. MD simulation on particles of experimental relevance takes huge computation time, despite using an expensive high-end server. Heterogeneous computing, a combination of the Field Programmable Gate Array (FPGA) and a computer, is proposed as a solution to compute MD simulation efficiently. In such heterogeneous computation, communication between FPGA and Computer is necessary. One such MD simulation, explained in the paper, is the (Artificial Neural Network) ANN-based IAP computation of gold (Au147 &amp

Au309) nanoparticles. MD simulation calculates the forces between atoms and the total energy of the chemical system. This work proposes the novel design and implementation of an ANN IAP-based MD simulation for Au147 &amp

Au309 using communication protocols, such as Universal Asynchronous Receiver-Transmitter (UART) and Ethernet, for communication between the FPGA and the host computer. To improve the latency of MD simulation through heterogeneous computing, Universal Asynchronous Receiver-Transmitter (UART) and Ethernet communication protocols were explored to conduct MD simulation of 50,000 cycles. In this study, computation times of 17.54 and 18.70 h were achieved with UART and Ethernet, respectively, compared to the conventional server time of 29 h for Au147 nanoparticles. The results pave the way for the development of a Lab-on-a-chip application. Copyright © 2024 The Authors. Published by Tech Science Press.