Accelerating\nMolecular Dynamics Simulations Using\nSocket-Based Interprocess Communication

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

Publication Details

Journal
Figshare
Published
2024-11-21
DOI
https://doi.org/10.1021/acs.jpclett.4c02860.s001
Primary Topic
Protein Structure and Dynamics
Type
article
Field-Weighted Citation Impact
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article

Accelerating\nMolecular Dynamics Simulations Using\nSocket-Based Interprocess Communication

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Protein Structure and Dynamics
article

Accelerating\nMolecular Dynamics Simulations Using\nSocket-Based Interprocess Communication

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Abstract

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

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Protein Structure and Dynamics
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