Data and code for molecular dynamics simulations in Substrate recognition and allosteric inhibition of human betaine/GABA transporter 1

Molecular Dynamics Reproducibility Package Description This repository contains the molecular dynamics reproducibility package associated with this study, including simulation input files, representative initial and final coordinate files, processed analysis outputs, and custom analysis/plotting scripts. Contents The package includes files associated with: 1. unbiased MD simulations of free BPDBA 2. binding cMD simulations 3. 2D metadynamics simulations 4. SMD, umbrella sampling, and WHAM/PMF analyses Files provided The repository includes, where applicable: - initial and final coordinate files for representative simulations - simulation input files (.mdp, PLUMED input files, topology/parameter files) - window generation scripts for umbrella sampling workflows - shell scripts (.sh) for workflow execution and analysis pipelines - Python scripts (.py) for data processing, statistical analysis, and figure generation - processed .xvg files used for plotting in the corresponding plotting_scripts directories System information Detailed system setup information, including system composition, lipid species, ionic conditions, and other simulation parameters, is provided in the Methods and Supplementary Table 2 of the manuscript. Software Software versions are consistent with those reported in the manuscript. Simulations were performed using GROMACS 2025.4 interfaced with PLUMED 2.9.4. Python-based data processing and plotting were carried out using standard scientific Python packages. Notes Detailed simulation protocols, methodological descriptions, and analysis context are described in the Methods and Supplementary Information of the manuscript. This repository is intended to provide the files associated with reproducibility and analysis of the MD results reported in the study.