VMD-L Mailing List

From: Toni Giorgino (toni.giorgino_at_gmail.com)
Date: Thu Aug 25 2011 - 07:24:55 CDT

Hi,

concerning the computation of membrane thickness, you might find this
plugin useful: http://multiscalelab.org/utilities/DensityProfileTool . It
computes 1-D density profiles, so projecting a proper selection of atoms
(perhaps "name P") along Z you will get two clear peaks, whose distance you
can measure. As pointed out by Vlad, you will still have to decide on an
atom selection.

Best

T

On Thu, Aug 25, 2011 at 9:14 AM, Vlad Cojocaru <
vlad.cojocaru_at_mpi-muenster.mpg.de> wrote:

> **
> 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"<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>
>
>>
>> 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
>
> 

-- 
Toni Giorgino, PhD - toni.giorgino_at_gmail.com - fax +39 0382 1850209
Post-doctoral research fellow - Computational Biochemistry and Biophysics
Lab
Universitat Pompeu Fabra - Barcelona Biomedical Research Park (PRBB)
C/ Doctor Aiguader 88, 08003 Barcelona, Spain