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

[Yuhua Song]

Dear Gromacs user:

Are there someone can answer my question about the calculation of the area
per headgroup of lipid if there are the ions and samll molecules half
inserted in the bilayer systems?

Thanks,

Yuhua

----- Original Message ----- 
From: "Nuno R. L. Ferreira" <nunolf at ci.uc.pt>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, June 10, 2004 7:23 PM
Subject: Re: [gmx-users] area per headgroup for lipid,and volume per lipid -
Gromacs


> 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
>
> Regards
> Nuno
>
> > Thanks
> >
> > Yuhua
> >
> >
> >
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> -- 
> **********************************************
> Nuno Ricardo Santos Loureiro da Silva Ferreira
> Grupo de Química Biológica
> Departamento Química
> Universidade de Coimbra
> Portugal
> www.biolchem.qui.uc.pt
> **********************************************
> "Do not worry about your difficulties in maths.
>  I can assure you that mine are still greater."
>                                    emc2
>
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