[gmx-users] Average area per lipid

Stephen Dutz smdutz at csupomona.edu
Fri Feb 29 04:19:23 CET 2008

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!




Stephen Dutz

Department of Chemistry &

Center for Macromolecular Modeling and Materials Design 

California State Polytechnic University, Pomona




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