[gmx-users] Lipid area calculation

[Yuhua Song]

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?

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
> > please help me out?
> 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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