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.本数据集包含与《Accelerating Molecular Dynamics Simulations using Fast Ewald Summation with Prolates》（采用长椭球快速埃瓦尔德求和加速分子动力学模拟）中所述的ESP分子动力学研究相关的基准测试数据、输入文件与可复现性数据。其涵盖经预处理的分子体系、拓扑文件、坐标文件、参数文件、模拟输入文件，以及用于在GROMACS和LAMMPS中对比基于ESP的静电学求解方法与基于PME (Particle Mesh Ewald)和PPPM (Particle-Particle Particle-Mesh)的参考工作流的作业脚本及相关测试用例。 本数据集按多个典型分子体系与基准测试组进行组织，涵盖本体水、锂离子电解质、溶菌酶蛋白、跨膜膜体系，以及一套完整的gromacs_bench基准集合。gromacs_bench目录包含误差分析用例、单核基准测试、强扩展性测试、膜与核糖体相关的扩展性基准测试，以及斜方盒体系可复现示例，如菱形十二面体RNA体系与截角八面体CONA体系。该归档文件包含.gro、.pdb、.top、.itp、.mdp、.tpr格式文件、Shell脚本、Slurm脚本及辅助元数据文件。 本数据集作为配套数据，与对应的ESP软件/代码发布版本一同提供。配合配套软件归档文件，这些文件可复现该研究中所述的基准测试搭建、力场误差评估与并行性能实验。部分子目录还包含溯源记录、README文件，以及当大型预生成配置集资源单独分发时的download_link.txt下载链接指引。