[gmx-users] Average area per lipid
mark.abraham at anu.edu.au
Fri Feb 29 04:59:48 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.
There's no need to involve VMD to get coordinates, and nobody on here is
likely to know how VMD will behave in such a case. trjconv allows you to
convert a trajectory so that the coordinates have PBC-properties that are
friendly for your analysis, and that plus a suitable index file to choose
the atomic coordinates of relevance has to be a good start. How to then
get your coordinates into a format for Mathematica for this tesselation is
probably a pertinent question though. gmxdump and a perl script are
probably the way forward - or even the same VMD process you were using.
> 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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