Accelerating molecular dynamics simulations using fast Ewald summation with prolates

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. Long-range electrostatic calculations are an expensive step in molecular dynamics simulations. Here, the authors introduce Ewald summation with prolates (ESP), which accelerates this step by up to tenfold, and implement it in open-source packages LAMMPS and GROMACS.