VMD-L Mailing List

From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Thu Aug 01 2013 - 11:26:58 CDT

On 8/1/2013 9:10 AM, Vita Duka wrote:
>
> Hello,
>
> I’m working with the synthesized cationic lipid MD simulations. During
> MD fthis lipid forms a tubular micellae, if started from a lipid
> bilayer (MD done with Amber 8.0). I would like to calculate average
> area per lipid headgroup.
>
> I have read in some previous posts in VMDlist and in papers about
> calculation methods and techniques but only for lipid bilayer
> structure. Can such calculations be done also for other lipid
> structural phases? I’m not a chemist and quite new with molecular
> modeling.
>
> Maybesomeone can suggest where to search or how to calculate the
> average area per lipid for tubular micellae with VMD? I have spent a
> lot of time searching for information and experimenting with script
> writing in VMD.
>
> T
>
Area per lipid is simply surface area divided by the number of lipids.
A simple calculation would be to determine the surface area of your
cylinder via pi*d*h and divide by the number of lipids in the outer
leaflet. That will get you in the ballpark, but keep in mind this is an
obvious approximation since it's unlikely you will actually get a
perfect cylinder.

Voronoi tessellation would be another route to get APL. It seems it
could be used to give you a reasonable estimate of the area per lipid
for bilayers of arbitrary geometry.

http://jcp.aip.org/resource/1/jcpsa6/v109/i4/p1517_s1 

-- 
======================================================================
Jeffrey J. Potoff                         jpotoff_at_wayne.edu
Associate Professor and Director of Early Engineering Programs
Department of Chemical Engineering and Materials Science
Wayne State University			  5050 Anthony Wayne Dr
Detroit, MI 48202
http://potoff1.eng.wayne.edu
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