Abstract
The evaluation of long-range Coulomb interactions is a significant cost in molecular dynamics (MD), even when using Particle Mesh Ewald (PME) or Particle-Particle-Particle-Mesh (PPPM) methods, which rely on Ewald splitting and the fast Fourier transform to achieve near-linear scaling. We introduce ESP—Ewald summation with prolate spheroidal wave functions (PSWFs)—which leads to a more efficient Fourier representation and a reduction in the required grid size, global communication, and particle-grid operations, without loss of accuracy. We have integrated the ESP method into two widely-used open-source MD packages, LAMMPS and GROMACS, enabling rapid comparison and adoption. Relative to PME/PPPM baselines at error tolerances 10−3 to 10−4, ESP gives roughly a 3-fold acceleration of electrostatic interactions, and a 2.5-fold speed-up in the MD simulation when using about 103 compute cores. At high accuracy (10−5), these increase to 10-fold for the far-field electrostatics and 5-fold for MD simulation. Furthermore, we show that the accelerated codes have improved strong scaling with core count, and validate them in realistic long-time biological and material simulations. ESP thus offers a practical, drop-in path to reduce the time-to-solution and energy footprint of MD workflows.
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Acknowledgements
The authors are grateful for discussions with Pilar Cossio and Berk Hess. They thank the Scientific Computing Core at the Flatiron Institute for support and for providing computational resources. The Flatiron Institute is a division of the Simons Foundation. J.L. discloses support for the research of this work from the National Natural Science Foundation of China (Grant No. 12401570) and the China Postdoctoral Science Foundation (Grant No. 2024M751948). All other authors declare no relevant funding.
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Liang, J., Lu, L., Barnett, A. et al. Accelerating molecular dynamics simulations using fast Ewald summation with prolates. Nat Commun (2026). https://doi.org/10.1038/s41467-026-73232-8
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DOI: https://doi.org/10.1038/s41467-026-73232-8
