GridMAT-MD: A grid-based membrane analysis tool for use with molecular dynamics

Abstract

GridMAT-MD is a new program developed to aid in the analysis of lipid bilayers from molecular dynamics simulations. It reads a GROMACS coordinate file and generates two types of data: a two-dimensional contour plot depicting membrane thickness, and a polygon-based tessellation of the individual lipid headgroups. GridMAT-MD can also account for proteins or small molecules within the headgroups of the lipids, closely approximating their occupied lateral area. The program requires no installation, is fast, and is freely available. © 2008 Wiley Periodicals, Inc.