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

[sameer varma]

One possible strategy:
1. Extract only headgroups
2. Project them on an XY plane (basically ignore Z)
3. Discretize on a 2-d grid
4. Count the number of boxes.
5. Or instead of steps 3 and 4: run through all relevant XY points and 
check if they are within radial distance from any headgroup atom: if yes, 
increment area
6. divide total area by number of lipids

At 09:58 AM 6/11/2004 -0500, you wrote:
>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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