[gmx-users] Lipid area calculation

[David]

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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