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.