[gmx-users] Area of Mixed lipid Bilayer

[ABEL Stephane 175950]

Hello, 

In addition with GridMat MD, you could use APL at Voro that reads the xtc trajectory and plots the average area per lipid. The program uses the Voronoi tesslation approach to compute the APL as it suggested by César Vila

 http://www.aplvoro.org/

Good luck 

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Message: 5
Date: Fri, 07 Mar 2014 10:35:28 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Area of Mixed lipid Bilayer
Message-ID: <5319E740.1030905 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 3/7/14, 10:31 AM, Nikhil Agrawal wrote:
> Dear All,
>
> I have assembled the mixed bilayer of POPC, POPE and Cardiolipin molecules.
> I want calculate the area of each lipid in the bilayer separately. Can
> anyone would suggest me how I would do that ?
>

<shameless self-promotion>

http://www.bevanlab.biochem.vt.edu/GridMAT-MD/

</shameless self-promotion>

There are a number of algorithms that will do this, ranging from our simple
grid-based approach to more complex Voronoi algorithms.  Several are published.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================


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Message: 6
Date: Fri, 7 Mar 2014 12:39:58 -0300
From: C?sar ?vila <clavila at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Area of Mixed lipid Bilayer
Message-ID:
        <CAKz=r7LHJN73VsQerxB87qTJ3Vb=xS1cJOPOFd-RHtFMKhcffw at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Using Voronoi Tesselation you can estimate the area occupied by each
molecule.
Cheers,
Cesar


2014-03-07 12:31 GMT-03:00 Nikhil Agrawal <nikhil.08oct at gmail.com>:

> Dear All,
>
> I have assembled the mixed bilayer of POPC, POPE and Cardiolipin molecules.
> I want calculate the area of each lipid in the bilayer separately. Can
> anyone would suggest me how I would do that ?
>
>
> Thanks in advance
>
>
>
> --
> Nikhil Agrawal
> Project Fellow
> Institute of Genomic & Integrative Biology (IGIB)
> Mathura Road
> New Delhi 110020
> --
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