Simulation Input Data for "Molecular simulation of lignin-related aromatic compound permeation through Gram-negative bacterial outer membranes"

This is the reduced data behind an upcoming manuscript investigating permeability across the outer membranes of Gram-negative bacteria. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was: <pre><code class="language-bash">tar --exclude="*BAK" --exclude="*dcd" --exclude="*xsc" --exclude="*vel" --exclude="*coor" --exclude="*csv" --exclude="*old" --exclude="*log" --exclude="*state" --exclude="*watpos/*npz" --exclude="*new*png" --exclude="*frame*png" --exclude="*ppm" --exclude="*mp4" --exclude="*bayesdata*npy" --exclude="*run.npy" -zcvf OM.tgz OuterMembrane</code></pre> Within the OuterMembrane directory, there are 3 primary subdirectories. <strong>Build </strong>contains the scripts and files to build the simulation systems, including the CHARMM-GUI output <strong>Equilibrium</strong> contains the equilibrium simulation inputs and the analysis scripts (subdirectory <strong>Analysis</strong>) <strong>REUS2</strong>, which has the replica exchange inputs and essential output. It also contains an <strong>Analysis</strong> subdirectory that carries out the analysis within the text.本数据集为一篇待发表论文的配套精简数据，该论文聚焦革兰氏阴性细菌外膜的通透性特性研究。本数据直接源自包含模拟与分析流程的原始目录结构，为适配Zenodo平台的上传容量限制，已剔除轨迹文件与中间产物文件。生成此压缩包所用的tar命令如下： <pre><code class="language-bash">tar --exclude="*BAK" --exclude="*dcd" --exclude="*xsc" --exclude="*vel" --exclude="*coor" --exclude="*csv" --exclude="*old" --exclude="*log" --exclude="*state" --exclude="*watpos/*npz" --exclude="*new*png" --exclude="*frame*png" --exclude="*ppm" --exclude="*mp4" --exclude="*bayesdata*npy" --exclude="*run.npy" -zcvf OM.tgz OuterMembrane</code></pre> 在OuterMembrane目录下，共包含3个核心子目录： **Build（构建目录）**：存放用于构建模拟系统的脚本与相关文件，其中包含CHARMM-GUI的输出结果； **Equilibrium（平衡模拟目录）**：存放平衡模拟的输入文件与分析脚本，其下设有子目录**Analysis（分析子目录）**； **REUS2（副本交换模拟目录）**：存放副本交换模拟的输入文件与核心输出结果，其下同样设有**Analysis（分析子目录）**，用于完成论文正文中的数据分析工作。