Exploring Natural Language Processing Model Acceleration in Molecular Dynamics Simulation Using High-Performance Computing and Machine Learning

In molecular dynamics simulations, the integral methods used to calculate molecular trajectories, such as the Verlet integral method, involve significant computational costs. On the premise of ensuring the accuracy of simulation, how to effectively reduce the amount of computation is always a challenging problem. This paper applies Natural Language Processing models to simulate molecular motion trajectories in molecular dynamics, integrating the MPI programming model and machine learning on a high-performance computing platform to achieve MPI parallelization during model training and inference. The results indicate that different types of neural network architectures have a significant impact on inference performance and accuracy. When using the deep spatio-temporal networks model, the mean absolute error is 0.0032. At an atomic scale of 3M, the parallel efficiency with 1024 computational nodes exceeds 90%, demonstrating excellent parallel performance.