title: APL@Voro: a Voronoi-based membrane analysis tool for GROMACS trajectories.
abstract: 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.
authors.affiliation: Bio-/Medical Informatics Department, University of Bielefeld , Universitätsstr. 25, 33615 Bielefeld, Germany.
authors.forename: Gunther
authors.initials: G
authors.lastname: Lukat
authors.forename: Jens
authors.initials: J
authors.lastname: Krüger
authors.forename: Björn
authors.initials: B
authors.lastname: Sommer
mesh_terms: D002784:Cholesterol / Q000737:chemistry*; D003196:Computer Graphics; D057225:Data Mining; D020407:Internet; D008051:Lipid Bilayers / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010713:Phosphatidylcholines / Q000737:chemistry*; D010714:Phosphatidylethanolamines / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry; D012984:Software
chemical_list: D008051:Lipid Bilayers; D010713:Phosphatidylcholines; D010714:Phosphatidylethanolamines; D011506:Proteins; C007510:1,2-dipalmitoyl-3-phosphatidylethanolamine; D002784:Cholesterol