[gmx-users] area per headgroup for lipid, and volume per lipid - Gromacs

Nuno R. L. Ferreira nunolf at ci.uc.pt
Fri Jun 11 02:23:41 CEST 2004

On Thursday 10 June 2004 12:13 am, Yuhua Song wrote:
> Hi, Eric:
> I had read your paper titled " Mesoscopic undulations and thickness
> fluctuation in lipid bilayers from molecular dynamcis simulaitons"
> published on Biophysical Journal Volume 79 July 2000, P426-433. In the
> paper, you have reported projected area and volume per lipid for 3
> different size systems for DPPC simulated with Gromacs.  Now, I am
> analyzing my MD data ( run with Gromacs), I am trying to figure out how to
> get the change of the area per headgroup, and volume of lipid during the
> 10ns simulaiton with Gromacs tools.
> Could you kindly let me know your ways to get the change of the area per
> headgroup, and volume of lipid during the simulation? Your help is grately
> appreciated.

IMHO, to calculate the volume per lipid you could do a MD run (same 
temperature and pressure used in your bilayer run) with a system with the 
same ratio of water/ions, and then calculate the specific volume for your 
ions and the water molecule. Then , 

(V.total - V.ions - V.water ) / total number lipids = Volume per lipid

where V. = volume


> Thanks
> Yuhua
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Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica 
Departamento Química
Universidade de Coimbra
"Do not worry about your difficulties in maths.
 I can assure you that mine are still greater."

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