GridMAT-MD:Examples



Welcome to the image gallery! We've posted a few representative images that showcase the utility of GridMAT-MD. Grid images have been rendered with Xmatrix, and protein images with Chimera. Analysis time benchmarks shown are based on performance on a 2.4 GHz Intel Core 2 Duo MacBook laptop with 2 GB RAM.

Analysis of P-P bilayer thickness for the 128-lipid DPPC bilayer available from Tieleman's site. The color scheme concisely shows fluctuations in the thickness across the bilayer in the x-y plane (unit cell dimensions shown in all figures, in nm), giving an overall impression of the average thickness, but still providing a nice level of detail about the bilayer.

Grid resolution: 20 x 20

Analysis time: 4 seconds.
The same bilayer as in the image above, analyzed with respect to area per lipid headgroup. Increased grid resolution relative to the thickness measurements yields polygons that correspond to each lipid head in the bilayer. The color scheme in this image is essentially meaningless, but is shown to illustrate the polygons. As described in the Algorithm page, each lipid headgroup is assigned a thickness value, from which its contribution to the lateral area is determined.

Grid resolution: 200 x 200

Analysis time: 2 minutes.
Area per lipid headgroup in the presence of a protein, in this example OmpA in DPPC. The bilayer contains roughly 500 lipids. This illustration shows how the area of the protein area (red and green) is subtracted from the lateral area of the bilayer. The two colors corresponding to the protein are indicative of the asymmetry of the protein, whose loop regions extend throughout the interface region of the top leaflet of the bilayer. There are no assumptions for "ideal" cylinders or other shapes - different areas can be subtracted from each leaflet when calculating the APL values. The protein is shown for reference.

Grid resolution: 200 x 200

Analysis time: 20 minutes.


Tesselation of a membrane system containing an unstructured, asymmetrically-oriented peptide that crosses periodic boundaries. Polygons are colored according to their Z-values, and the protein is colored in red. The image demonstrates the ability of GridMAT-MD to calculate areas for even the most difficult systems, including the area for a protein that has unfolded at the membrane interface.

Grid resolution: 200 x 200

Analysis time: 5 minutes.


GridMAT-MD Home
Bevan Lab Homepage

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