Molecular dynamics simulation data for β-cyclodextrin complexes with ursodeoxycholic acid and cholic acid

This dataset contains molecular dynamics simulation inputs, coordinates, topology and force-field files, simulation logs, analysis scripts, and production trajectories for β-cyclodextrin complexes with ursodeoxycholic acid (UDCA) and cholic acid (CA). Eight initial insertion depths (D0–D7, 0.0–0.7 nm) were investigated for each bile acid, defining 16 simulation conditions. Three independent simulations of 200 ns were performed for each condition, resulting in 48 production simulations and a total production simulation time of 9.6 μs. The simulations were performed using GROMACS 2024.3. Version 1 contains the core files for the original set of 16 simulations, including simulation inputs, initial and final coordinates, topology and force-field files, logs, and analysis scripts. Version 2 retains the Version 1 archive and adds two independent repeats (Repeat 2 and Repeat 3) for all 16 conditions. The 32 additional 200 ns production trajectories are provided as individual XTC files. A supporting-files archive contains their associated GROMACS inputs, topology and parameter files, equilibration and production outputs, final structures, run logs, scripts, and completion records. A README describes the file organization, and SHA-256 checksums are provided for integrity verification.