APL@Voro: a Voronoi-based membrane analysis tool for GROMACS trajectories

Area of Science:

• Computational biophysics
• Molecular dynamics simulations
• Bioinformatics

Background:

• Analyzing lipid bilayer simulations requires specialized tools for geometric interpretation.
• Existing methods may not fully capture the complexity of mixed lipid and protein bilayers.
• Accurate calculation of properties like projected area per lipid is crucial for understanding membrane behavior.

Purpose of the Study:

• To introduce APL@Voro, a novel software for analyzing GROMACS lipid bilayer simulations.
• To provide advanced tools for geometric analysis using Voronoi diagrams and Delaunay triangulations.
• To support the study of complex lipid bilayers containing various lipids and proteins.

Main Methods:

• The program reads GROMACS trajectory, PDB coordinate, and index files.
• It generates 2D geometric representations using Voronoi diagrams and Delaunay triangulations.
• Modified Voronoi approaches and new triangulation methods are implemented for accurate calculations.

Main Results:

• APL@Voro successfully creates 2D geometric representations of bilayers.
• It enables visualization, plotting, and export of calculated values from geometric structures.
• The software handles complex bilayers with mixed lipids and proteins effectively.

Conclusions:

• APL@Voro offers a user-friendly, open-source solution for detailed lipid bilayer analysis.
• The implemented methods enhance the accuracy of projected area per lipid calculations.
• This tool facilitates deeper insights into the structure and dynamics of biological membranes.