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GridMAT‐MD: A grid‐based membrane analysis tool for use with molecular dynamics
Author(s) -
Allen William J.,
Lemkul Justin A.,
Bevan David R.
Publication year - 2009
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21172
Subject(s) - molecular dynamics , polygon (computer graphics) , grid , plot (graphics) , computer science , computational science , membrane , lipid bilayer , tessellation (computer graphics) , chemistry , computer graphics (images) , biological system , computational chemistry , geometry , mathematics , biology , biochemistry , telecommunications , statistics , frame (networking)
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. J Comput Chem, 2009