GridMAT-MD

Grid-based Membrane Analysis Tool for use with Molecular Dynamics



New Release (4/18/2013): Version 2.0 is now available! Please see the release notes.

Developers

Algorithm

Examples

Bug Fixes

Download

GridMAT-MD is a simple program, written in Perl, designed to analyze two important parameters in simulations of lipid bilayers - area per lipid headgroup (APL) and bilayer thickness. The program is particularly useful in the case of an embedded membrane protein, as the program can calculate the APL, while still compensating for the lateral area occupied by the protein at the intersection with the membrane interface.
We are making GridMAT-MD available to the public, free of charge, under the terms and conditions of the GNU Public License (GPL). A copy of the license is included with the program. Click "Download" to get a copy of GridMAT-MD! Documentation is included, but if you just want a copy of the most up-to-date User's Guide, it can be downloaded separately here.

We hope that you will find GridMAT-MD useful. We believe it to be superior to most current methods of analyzing simulated bilayers and membrane protein systems for several reasons:
  • It requires no installation; as long as a Perl interpreter is installed on your system (which is true for most modern Unix, Linux, and Mac systems), GridMAT-MD will run.
  • It makes no approximations of "ideal proteins," calculating the area occupied by your protein in each leaflet of the bilayer.
  • It does not require expensive commercial software.
  • It's fast! Typical thickness calculations run in under 10 seconds, and APL calculations in 3-5 minutes. For very large systems, take note that calculation time scales with system size, so if you have several thousand lipids, have some coffee and come back later!
Should you encounter difficulties, contact one of the developers, and we will do our best to help. Please realize that this is free software, and we do not imply any warranty or guarantee any technical support. If you have ideas, questions, comments, or if you have made useful modifications to the code, please send them to us! We welcome feedback and user contributions.

A parallel version of GridMAT-MD has been developed by a GridMAT-MD user and is avaliable here.

If you download GridMAT-MD and use it in any publications, we ask that you cite the following reference:

W. J. Allen, J. A. Lemkul, and D. R. Bevan. (2009) "GridMAT-MD: A Grid-based Membrane Analysis Tool for Use With Molecular Dynamics." J. Comput. Chem. 30 (12): 1952-1958.

Bevan Lab Homepage


Site design copyright 2008-2011 by Justin Lemkul
Questions? Problems with the site? Comments? Send them to the Webmaster