Example Dataset of Molecular Dynamics Simulations for MeTrEx

This data set contains an example of Molecular Dynamics (MD) Simulation files. A Pseudomonas aeruginosa membrane was simulated with Polymyxin B1 and used as an example data set for MeTrEx (Membrane Trajectory Explorer). MeTrEx is a Python-based software to explore and analyse MD Simulation ligand and membrane molecule interaction data.

The manuscript is currently under review, and the data set will be published open-source after acceptance.

Included Files

1. example_topology_with_6PMB.pdb

Description: Structure file in PDB format, including the topology of a membrane system with six polymyxin B (PMB) molecules.

Purpose: Provides the structural data required to initialise the simulation.

2. example_simulation_6PMB_5000Frames.xtc

Description: Trajectory file in XTC format containing 5,000 frames of a PMB-membrane interaction simulation.

Purpose: Allows detailed trajectory exploration and visual analysis in MeTrEx.

3. example_simulation_6PMB_500Frames.xtc

Description: A shorter trajectory file (500 frames) for rapid testing and exploration.

Purpose: Serves as a lightweight example for quick demonstrations.

4. example_contact_LH0_PMB.xvg

Description: XVG file providing contact analysis data between PMB molecules and the upper membrane leaflet lipids (LH0).

5. example_membrane_solvent.xvg

Description: XVG file containing analysis data of membrane solvent properties.

How to Use

1. Import the provided files into MeTrEx for the visualisation and analysis workflow.

2. Explore trajectory visualisation, molecular speed and distance mapping, and external analysis integration (XVG File analysis) using the software's corresponding tools.

3. Refer to the MeTrEx documentation for step-by-step guidance on loading and interacting with these datasets.

If you have questions or need support, please contact the MeTrEx developers or refer to the official documentation.

本数据集包含分子动力学（Molecular Dynamics, MD）模拟文件示例。本次模拟以搭载多粘菌素B1（Polymyxin B1）的铜绿假单胞菌（Pseudomonas aeruginosa）膜系统为对象，作为MeTrEx（膜轨迹探索器，Membrane Trajectory Explorer）的示例数据集。MeTrEx是一款基于Python开发的软件，用于探索与分析MD模拟中的配体与膜分子相互作用数据。

本手稿目前处于审稿阶段，数据集将在录用后以开源形式公开发布。

### 包含文件
1. example_topology_with_6PMB.pdb
格式说明：PDB格式结构文件，包含搭载6个多粘菌素B（PMB）分子的膜系统拓扑结构。
用途：提供初始化模拟所需的结构数据。

2. example_simulation_6PMB_5000Frames.xtc
格式说明：XTC格式轨迹文件，包含5000帧PMB-膜相互作用模拟轨迹。
用途：支持在MeTrEx中开展精细化轨迹探索与可视化分析。

3. example_simulation_6PMB_500Frames.xtc
格式说明：精简版轨迹文件（仅500帧），用于快速测试与探索。
用途：作为轻量化示例用于快速演示与验证。

4. example_contact_LH0_PMB.xvg
格式说明：XVG格式文件，提供PMB分子与上层膜脂小叶（LH0）之间的接触分析数据。

5. example_membrane_solvent.xvg
格式说明：XVG格式文件，包含膜系统溶剂特性的分析数据。

### 使用方法
1. 将提供的文件导入MeTrEx，即可启动可视化与分析工作流。
2. 通过软件内置工具实现轨迹可视化、分子速率与距离映射，以及外部分析集成（XVG文件分析）功能。
3. 请参阅MeTrEx官方文档，获取加载与交互此类数据集的分步操作指南。

如有疑问或需要技术支持，请联系MeTrEx开发团队或参阅官方文档。