GridMAT-MD: A Grid-Based Membrane Analysis Tool for Use With Molecular Dynamics

被引：264

作者：

Allen, William J. ^{[1
]}

Lemkul, Justin A. ^{[1
]}

Bevan, David R. ^{[1
]}

机构：

[1] Virginia Polytech Inst & State Univ, Dept Biochem, Blacksburg, VA 24061 USA

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2009年 / 30卷 / 12期

基金：

美国国家科学基金会;

关键词：

Lipid bilayer analysis; molecular dynamics; lipid bilayer thickness; area per lipid headgroup; tessellation; PARTICLE MESH EWALD; LIPID-BILAYERS; PROTEIN SIMULATIONS; MODEL; PEPTIDES;

D O I：

10.1002/jcc.21172

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

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. (C) 2008 Wiley Periodicals, Inc. J Comput Chem 30: 1952-1958, 2009

引用

页码：1952 / 1958

页数：7

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