Work

Accelerating Molecular Dynamics Simulations Using Socket-Based Interprocess Communication

Year: 2024

Type: article

Abstract: Molecular dynamics (MD) simulations are essential for studying the time evolution of molecular systems. Still, their efficiency is often bottlenecked by file-based interprocess communication (IPC) between MD and electronic structure programs. We present a socket-based IPC implementation that dramatically accelerates MD simulations, reducing the computational time by >10-fold compared to those of traditional file-based methods. Our approach, applied to nonadiabatic molecular dynamics with the Newton-X program, eliminates disk read/write overhead, allowing for faster simulations over longer time scales. This method opens the door to more efficient high-throughput simulations, providing new opportunities for exploring complex molecular processes in real time.

Source: The Journal of Physical Chemistry Letters

DOI: 10.1021/acs.jpclett.4c02860

Authors: Matheus de Oliveira Bispo, Mario Barbatti

Institutions: Centre National de la Recherche Scientifique, Aix-Marseille Université, Institut de Chimie Radicalaire, Institut Universitaire de France

Language: English

Topic: Parallel Computing and Optimization Techniques

Subfield: Hardware and Architecture

Field: Computer Science

Domain: Physical Sciences

Open Access status: green

Funders: Aix-Marseille Université, Fondation Aix-Marseille Universite, European Research Council, H2020 European Research Council

Awards: Computational Photochemistry in the Long Timescale: Sub-ns Photoprocesses in DNA, G5128154969, G5918387807, G6039209223, G93802840