# [gmx-users] Lipid area calculation

David spoel at xray.bmc.uu.se
Mon Nov 10 20:30:01 CET 2003

```On Mon, 2003-11-10 at 20:13, Yuhua Song wrote:
> Thanks David. I use the way that you describe to calculated the lipid area,
> I gets the reasonable lipid area. From the literature, its seems that
> another parameter need to validate is volume/lipid. Now, I have box_x,
> box_y, box_z, I get the total volume. if I want to calcuate the
> volume/lipid, I assume that I shoud be: (total volume-water volume)/#total
> lipids. Am I right? If I am right, how could get the water volume? from
> literature, it said that SPC water 1.03g cm^-3 at 323 K. Now, I only know
> that number of water in my system, how can I know one water volume? If my
> way to calculate the volume/lipd is not right. Could you please give me some
> suggestion?
>
I don't think we have a tool to do it straight off. The algorithm is
simple though. Sample random points in your box, and count how many of
them are inside the lipids. This gives you the fraction of the volume in
the box.

Other algorithms include more fancy things combined with e.g. surface
area calculations.

> Thanks,
>
> Yuhua
>
>
>
>
>
> ----- Original Message -----
> From: "David" <spoel at xray.bmc.uu.se>
> To: <gmx-users at gromacs.org>
> Sent: Sunday, November 09, 2003 6:32 PM
> Subject: Re: [gmx-users] Lipid area calculation
>
>
> > On Sun, 2003-11-09 at 22:55, Yuhua Song wrote:
> > > Hi, Gromacs developer and users:
> > >
> > > After I  equilibrate a 64 DPPC bilayer (download from peter's website),
> I intend to calculate the lipid area for
> > > validation, the experimental value of a DPPC bilayer should be around
> 0.61nm^2
> > >
> > > My way to calculate the lipid area is:
> > > 1) to make index file for one DPPC
> > > 2) use g_sas to calculate one DPPC area. The results shows as below, it
> seems that
> > > it has nothing to do with 0.61nm^2 standard value.
> > >
> > > I do not know what is wrong. My way to calculate the lipid area is
> wrong? could you
> > You take simply box-x times box-y / #lipids per monolayer
> > >
> > > Thank you very much. Yuhua
> > >
> > >
> > > # This file was created by
> /home/soft/cluster/gromacs/i686-pc-linux-gnu/bin/g_sas
> > > # which is part of G R O M A C S:
> > > # Good gRace! Old Maple Actually Chews Slate
> > > # All this happened at: Sun Nov  9 21:37:12 2003
> > > #
> > > @    title "Solvent Accessible Surface"
> > > @    xaxis  label "Time (ps)"
> > > @    yaxis  label "Area (nm\S2\N)"
> > > @TYPE xy
> > > @ view 0.15, 0.15, 0.75, 0.85
> > > @ legend on
> > > @ legend box on
> > > @ legend loctype view
> > > @ legend 0.78, 0.8
> > > @ legend length 2
> > > @ s0 legend "Hydrophobic"
> > > @ s1 legend "Hydrophilic"
> > > @ s2 legend "Total"
> > > @ s3 legend "D Gsolv"
> > >          0     19.2265     9.33045      28.557           0
> > >       0.05     19.0852     9.38099     28.4662           0
> > >        0.1     19.2972     9.25305     28.5503           0
> > >       0.15     19.2265     9.24634     28.4729           0
> > >        0.2     19.3326     9.24634     28.5789           0
> > >       0.25     19.3326     9.21771     28.5503           0
> > >        0.3     19.4386     9.38315     28.8218           0
> > >       0.35     19.4386     9.36124     28.7998           0
> > >        0.4     19.2972     9.31702     28.6143           0
> > >       0.45     19.2619     9.34565     28.6075           0
> > >        0.5     19.2972     9.23114     28.5284           0
> > >       0.55     19.1912     9.43825     28.6295           0
> > >        0.6     19.2972     9.41178      28.709           0
> > >       0.65     19.3679     9.29511      28.663           0
> > >        0.7     19.3679     9.35908      28.727           0
> > >       0.75     19.3326     9.31702     28.6496           0
> > >        0.8     19.4033      9.2329     28.6362           0
> > >       0.85     19.1559     9.21315      28.369           0
> > >        0.9     19.3679     9.18236     28.5503           0
> > >       0.95     19.2265     9.20428     28.4308           0
> > >          1     19.2972     9.41633     28.7136           0
> > >       1.05     19.3326     9.40114     28.7337           0
> > >        1.1     19.0498     9.55315      28.603           0
> > >       1.15     19.1559     9.31031     28.4662           0
> > >        1.2     19.3679     9.28839     28.6563           0
> > >       1.25     19.1205     9.21987     28.3404           0
> > >        1.3     19.2265     9.21099     28.4375           0
> > >       1.35     19.3679     9.28168     28.6496           0
> > >
> > >
> > > _______________________________________________
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> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,  75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
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>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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