VMD-L Mailing List

From: Stephen Dutz (smdutz_at_csupomona.edu)
Date: Mon Mar 03 2008 - 11:14:11 CST

Hi all,

I'm using gromacs for MD simulations on membrane proteins. As part of the analysis I would like to calculate the average area per lipid. I've been going about this by pulling the coordinates from the trajectory in VMD, then importing these to Mathematica and using it to plot a voronoi tessellation. The problem I run in to is I have to discard ~10% of the data (when averaging over multiple frames) due to Mathematica not being able to complete the tessellation. I believe this is occurring as a result of PBC and Mathematica plotting concave polygons. That being said, I have just about given up on my method.

I was wondering if anyone out there has a script or methodology they would be willing to share with me in order to calculate the area per lipid with a protein present (i.e using a voronoi tessellation). I would appreciate it tremendously!

Sincerely,

Stephen Dutz

 
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