APL@Voro: A voronoi-based membrane analysis tool for GROMACS trajectories

Gunther Lukat, Jens Kruger, Bjorn Sommer

Research output: Contribution to journalArticleResearchpeer-review

45 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)2908 - 2925
Number of pages18
JournalJournal of Chemical Information and Modeling
Volume53
Issue number11
DOIs
Publication statusPublished - 2013
Externally publishedYes

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