Molecular dynamics simulation trajectories and analysis data for Foldback intercoil (FBI) DNA recombination intermediates

This archive contains the complete FBI molecular dynamics simulation dataset. The dataset includes representative structural models, curated GROMACS simulation input files, raw molecular dynamics trajectories, Python analysis scripts, processed figure source data, and file-level documentation. The archive covers the FBIbasic, FBIhetero, and FBIexchange simulation systems. The trajectories directory contains production and structure-generation trajectory files together with associated GROMACS run input, final coordinate, and parameter files where available. The analysis scripts were used to calculate P-P occupancy and P-P distance metrics. The processed CSV tables used for figure plotting are provided in figure_source_data. For P-P occupancy and P-P distance analyses, raw trajectories were processed for periodic-boundary-condition handling before distance calculation, including nojump and centering steps using gmx trjconv. The raw .xtc files should therefore be treated as the primary simulation trajectories, and the same PBC correction workflow should be applied when reproducing the plotted values from the trajectories. A SHA256 checksum file is included for file-integrity verification.本数据集涵盖针对FBIbasic、FBIhetero及FBIexchange三种DNA重组中间模型的分子动力学轨迹文件与配套GROMACS输入文件。该归档包含三组各50 ns的FBIbasic生产模拟副本、一组5 ns的FBIhetero结构生成轨迹、三组各50 ns的FBIhetero生产模拟副本、一套FBIexchange结构生成工作流，以及三组各50 ns的FBIexchange生产模拟副本。轨迹以原始GROMACS XTC文件形式提供，并附带对应可用的TPR、GRO及MDP文件。相关论文中报道的P-P占有率与P-P距离分析，均在经过周期性边界条件校正后完成。用于此类分析的处理后图像源数据与分析脚本，可从配套GitHub仓库获取：https://github.com/BBHH-byb/FBI_simulation_dataset。