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.