Example Dataset of Molecular Dynamics Simulations for MeTrEx

Abstract

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.