Simulation input and output files for: "Predicting residue ionization of OmpF channel using Constant pH Molecular Dynamics as benchmarking"

This dataset contains input and selected output files to reproduce one replica of the simulations described in the preprint: "Predicting residue ionization of OmpF channel using Constant pH Molecular Dynamics as benchmarking"Available at bioRxiv: https://doi.org/10.1101/2025.06.16.659857 The files are organized in the CpH-MD-DPPC directory and include: Parameter (.mdp) files for Constant-pH Molecular Dynamics (CpH-MD) simulations System topology and starting structure files (.top, .gro, etc.) Output .xvg files from gmx cphmd, containing lambda values used to derive titration curves Simulations were performed using a modified version of the GROMACS package that implements CpH-MD, available at:https://gitlab.com/gromacs-constantph/constantph Note: Full trajectory and log output files are not included here due to their large size. They are available upon reasonable request by contacting the corresponding author. This dataset is intended as a supplementary resource to facilitate reproducibility and further analysis.本数据集包含用于复现预印本中所述模拟副本的输入文件与精选输出文件，预印本题为《以恒定pH分子动力学为基准预测OmpF通道的残基电离特性》，可于bioRxiv获取：https://doi.org/10.1101/2025.06.16.659857。 文件收纳于CpH-MD-DPPC目录中，具体包含： 1. 用于恒定pH分子动力学（Constant-pH Molecular Dynamics, CpH-MD）模拟的参数文件（.mdp格式）； 2. 系统拓扑与初始结构文件（.top、.gro等格式）； 3. 由gmx cphmd生成的输出.xvg文件，其中包含用于推导滴定曲线的lambda值。 本模拟使用了实现CpH-MD功能的改良版GROMACS软件包，该版本可于https://gitlab.com/gromacs-constantph/constantph获取。 注意：由于完整轨迹与日志输出文件体积过大，本数据集未包含此类文件。若有合理使用需求，可联系通讯作者获取。 本数据集旨在作为补充资源，以助力研究的可复现性与后续分析工作。