Accelerating Molecular Dynamics Simulations using Fast Ewald Summation with Prolates
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arXiv
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| Main Authors: | , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866918452742062080 |
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| author | Liang, Jiuyang Lu, Libin Barnett, Alex Greengard, Leslie Jiang, Shidong |
| author_facet | Liang, Jiuyang Lu, Libin Barnett, Alex Greengard, Leslie Jiang, Shidong |
| contents | 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 $10^3$ 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2505_09727 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Accelerating Molecular Dynamics Simulations using Fast Ewald Summation with Prolates Liang, Jiuyang Lu, Libin Barnett, Alex Greengard, Leslie Jiang, Shidong Numerical Analysis Biological Physics 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 $10^3$ 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. |
| title | Accelerating Molecular Dynamics Simulations using Fast Ewald Summation with Prolates |
| topic | Numerical Analysis Biological Physics |
| url | https://arxiv.org/abs/2505.09727 |