APL@Voro was developed at the University of Bielefeld by Gunther Lukat. The Development would not have been possible without the great help and contributions of Dr. Jens Krüger (University Tübingen) and Dr. Björn Sommer (University Bielefeld).

APL@Voro is a program developed to aid in the analysis of GROMACS Molecular dynamics trajectories of lipid bilayer simulations. It deals with whole GROMACS trajectory files, PDB coordinate files and a GROMACS index files to create a two dimensional geometric representation of a bilayer. The analysis of the bilayer is supported by using the Voronoi diagrams and Delaunay triangulations generated for different selection models of lipids. The values calculated on the geometric structures can be visualized in an interactive environment, plotted and exported to different file types. APL@Voro supports complex bilayers with a mix of various lipids and proteins and calculates the area per lipid and the bilayer thickness. The program is written in C++, open source and published under the GPL 3.0 License. 

The development of APL@Voro is closely linked to the CELLmicrocosmos 2.2 MembraneEditor(CmME) project, with the initial aim to provide a software for micro domain detection in model membranes. During the research on bilayer systems, APL@Voro was further developed and became a complex software suit, rich of functions and with a wide range of application. 

The different options for plotting and the displayed Voronoi diagrams were helpful for us, and we decided to make it accessible to the community. 

The author wants to thank Dr. Björn Sommer and Dr. Jens Krüger; for their patience, the useful discussions and the hard work on testing APL@Voro.

If you use APL@Voro, please cite:

Kern, Martin; Jaeger-Honz, Sabrina; Schreiber, Falk; Sommer, Bjorn: APL@voro—interactive visualization and analysis of cell membrane simulations. Bioinformatics, 39(2) 2023, p.btad083.

Lukat, Gunther; Krüger, Jens; Sommer, Björn: APL@ Voro: a Voronoi-based membrane analysis tool for GROMACS trajectories. J Cheminform. 2013, 53(11):2908-25.

Happy Simulating! 

Author: Gunther Lukat