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.分子动力学可重复性包（Molecular Dynamics Reproducibility Package） 描述 本仓库包含本研究配套的分子动力学可重复性分析包，涵盖模拟输入文件、典型初始与最终坐标文件、处理后的分析结果文件，以及自定义的分析与绘图脚本。 内容 本包包含与以下内容相关的文件： 1. 游离BPDBA的无偏分子动力学（MD）模拟 2. 结合态常规分子动力学（cMD）模拟 3. 二维元动力学模拟 4. SMD、伞形采样，以及WHAM/PMF分析 提供的文件 本仓库在适用场景下提供以下文件： - 典型模拟的初始与最终坐标文件 - 模拟输入文件（.mdp、PLUMED输入文件、拓扑/参数文件） - 伞形采样工作流的窗口生成脚本 - 用于工作流执行与分析流水线的Shell脚本（.sh） - 用于数据处理、统计分析与图表生成的Python脚本（.py） - 对应plotting_scripts目录中绘图所用的已处理.xvg文件 系统信息 详细的系统搭建信息，包括系统组成、脂质种类、离子条件及其他模拟参数，已在本文的方法部分与补充表2中提供。 软件 软件版本与本文报道的版本保持一致。模拟工作使用GROMACS 2025.4，并与PLUMED 2.9.4联用完成。基于Python的数据处理与绘图工作采用标准科学计算Python包完成。 备注 详细的模拟流程、方法学描述与分析背景已在本文的方法部分与补充信息中阐明。本仓库旨在提供与本研究报道的分子动力学结果可重复性验证及分析相关的配套文件。