Membrane simulation analysis using Voronoi tessellation (Conference Abstract)

Lukat G, Sommer B, Krüger J. Membrane simulation analysis using Voronoi tessellation (Conference Abstract). In: Journal of Cheminformatics. Journal of Cheminformatics. Vol 6. Springer Science and Business Media LLC; 2014

APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories

APL@Voro is a new program developed to aid in the analysis of GROMACS trajectories of lipid bilayer simulations. It can read a GROMACS trajectory file, a PDB coordinate file, and a GROMACS index file to create a two-dimensional geometric representation of a bilayer. Voronoi diagrams and Delaunay triangulationsgenerated for different selection models of lipidssupport the analysis of the bilayer. The values calculated on the geometric structures can be visualized in a user-friendly interactive environment and, then, plotted and exported to different file types. APL@Voro supports complex bilayers with a mix of various lipids and proteins. For the calculation of the projected area per lipid, a modification of the well-known Voronoi approach is presented as well as the presentation of a new approach for including atoms into an existing triangulation. The application of the developed software is discussed for three example systems simulated with GROMACS. The program is written in C++, is open source, and is available free of charge

APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories

Lukat G, Krueger J, Sommer B. APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories. Journal Of Chemical Information And Modeling. 2013;53(11):2908-2925.APL@Voro is a new program developed to aid in the analysis of GROMACS trajectories of lipid bilayer simulations. It can read a GROMACS trajectory file, a PDB coordinate file, and a GROMACS index file to create a two-dimensional geometric representation of a bilayer. Voronoi diagrams and Delaunay triangulations-generated for different selection models of lipids-support the analysis of the bilayer. The values calculated on the geometric structures can be visualized in a user-friendly interactive environment and, then, plotted and exported to different file types. APL@Voro supports complex bilayers with a mix of various lipids and proteins. For the calculation of the projected area per lipid, a modification of the well-known Voronoi approach is presented as well as the presentation of a new approach for including atoms into an existing triangulation. The application of the developed software is discussed for three example systems simulated with GROMACS. The program is written in C++, is open source, and is available free of charge