[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
> > > 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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--
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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