From: Nuno Sousa Cerqueira (nscerque_at_fc.up.pt)
Date: Thu Aug 01 2013 - 18:29:57 CDT

http://www2.fc.up.pt/PortoBioComp/Software/Volarea/Home.html

On Thu, Aug 1, 2013 at 5:26 PM, Jeffrey Potoff <jpotoffx_at_gmail.com> wrote:

> 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
> ==============================**==============================**==========
>
>

-- 
Nuno M. F. Sousa A. Cerqueira
Chemistry Department
Faculty of Sciences
University of Porto
Rua do Campo Alegre, s/n
4169-007 Porto
Portugal
Tel: +351 220402501
Fax: +351 220 402 009
email: nscerque_at_fc.up.pt
website: http://www.fc.up.pt/pessoas/nscerque