VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu Aug 25 2011 - 02:14:15 CDT

Hi Clark,

Average area per lipid: "box size X * box size Y / no. of lipids"
(assuming your lipid is in the XY plane) ...
Local area per lipid: more complicated: a good starting point:
"http://jcp.aip.org/resource/1/jcpsa6/v109/i4/p1517_s1" (I am sure there
are other good references)

Thickness: bring the membrane center of mass at origin (0,0,0).
Calculate average positive Z coordinates and average negative Z
coordinates (assuming your lipid is in the XY plane). Substract the
negative from the positive average and you'll have. You can use
different atom selections (your choice depending of what thickness you
wish to calculate) for the calculation of average Z coordinates ...

If you wish, I can dig up the scripts I have been using to calculate
these in VMD (except for the local area per lipid).

Vlad

On 08/25/2011 08:41 AM, Boyang Wang wrote:
> Hi Yong,
> in VMD, there is a lipid membrane builder, where you can find the
> typical area per lipid and thickness for the lipid bilayer. Maybe in
> the reference of you paper, you can cite the VMD reference.
> Best,
> Boyang
>
> 2011/8/25 张勇 <clarkzhy_at_mail.bnu.edu.cn
> <mailto:clarkzhy_at_mail.bnu.edu.cn>>
>
>
> Hi everyone,
>
>
> Is there anyone here to know how to calculate the area per lipid
> and thickness for a lipid bilayer in a membrane-protein system?
>
> Or, could anyone share the scripts to calculte them?
>
> Any help will be highly appreciated!! Thanks in advance!
>
> Clark
>
>
>
>
>
>
> --
> Boyang Wang, Ph.D.
> 

-- 
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de
-- 
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de