MD Dataset for "Accelerating Molecular Dynamics Simulations using Fast Ewald Summation with Prolates"

This dataset contains the benchmark, input, and reproducibility data associated with the ESP molecular dynamics study described in “Accelerating Molecular Dynamics Simulations using Fast Ewald Summation with Prolates.” It includes prepared molecular systems, topology files, coordinate files, parameter files, simulation input files, and job scripts used to evaluate ESP-based electrostatics against PME- and PPPM-based reference workflows in GROMACS and LAMMPS and related test cases. The dataset is organized into several representative molecular systems and benchmark groups, including bulk water, Li-ion electrolyte, lysozyme protein, transmembrane membrane systems, and a comprehensive gromacs_bench collection. The gromacs_bench directory contains error-analysis cases, single-core benchmarks, strong-scaling tests, membrane and ribosome-related scaling benchmarks, and triclinic-box reproducibility examples such as Rhombic-dodecahedral RNA and Truncated-Ocahedral CONA systems. The archive includes files such as .gro, .pdb, .top, .itp, .mdp, .tpr, shell scripts, Slurm scripts, and auxiliary metadata files. This record is intended as the data companion to the associated ESP software/code release. Together with the companion software archive, these files support reproduction of benchmark setups, force-error evaluations, and parallel performance experiments reported in the study. Some subdirectories also include provenance notes, README files, and download_link.txt pointers for large pre-generated configuration sets when those assets are distributed separately.