[gmx-users] Re: Re: problem about g_sas of POPC bilayer
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jun 6 08:47:53 CEST 2008
minnale wrote:
>
> Thanks for your reply
> NO, I am having 64 lipids in each leaflet of bilayer.
> I want to calculate average area per lipid. what I have mentioned
> options are correct for g_sas?
for area you use the box X times box Y divided by 64.
g_sas gives you solvent accessibe surfce area
> Thanks for your appreciation
>
> innale wrote:
> > Hi all,
> > I have downloaded POPC bilayer from peter teileman,s website and
> > simulated for 5ns under anisotropic pressure coupling. When I drew a
> > potential energy plot its shown that system is stabilised, so I have
> > stopped the simulation at 5ns.
> > After that I have mentioned g_sas command for calculating surface area
> > of lipid in this way and got .xvg file like below mentioned
> >
> > command : g_sas -f 5ns_popc.xtc -s min_popc.tpr -pbc -o area_popc.xvg
> >
> > .xvg File:
> > @ 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"
> > 0 152.383 228.165 380.548 0
> > 0.2 149.279 230.277 379.555 0
> > 0.4 153.175 229.306 382.481 0
> > 0.6 149.312 229.188 378.499 0
> > 0.8 149.708 228.811 378.518 0
> > 1 149.972 229.69 379.662 0
> > 1.2 155.587 229.615 385.202 0
> > 1.4 151.953 227.696 379.649 0
> > 1.6 149.113 229.903 379.016 0
> > 1.8 151.062 227.394 378.456 0
> > 2 149.278 226.934 376.213 0
> > 2.2 151.095 225.68 376.774 0
> > 2.4 149.873 229.576 379.449 0
> > 2.6 148.387 230.391 378.778 0
> > 2.8 147.627 227.792 375.419 0
> > 3 148.156 229.589 377.745 0
> > 3.2 145.051 229.568 374.619 0
> > 3.4 147.231 229.814 377.044 0
> > 3.6 145.348 229.392 374.741 0
> > 3.8 148.717 229.43 378.146 0
> > 4 153.307 230.834 384.142 0
> > 4.2 153.604 230.6 384.204 0
> > 4.4 154.397 229.345 383.742 0
> > 4.6 155.718 230.864 386.582 0
> > 4.8 155.685 231.226 386.911 0
> > 5 152.911 231.332 384.243 0
> > 5.2 153.935 229.453 383.388 0
> > 5.4 154.43 231.396 385.826 0
> > .
> > .
> > .
> > .
> > .
> > till 5000ps.
> >
> > I have searched in gmx-archives about SAS of lipid, I found that lipid
> > SAS should be 0.64 nm^2/sec but I got values range from 150 to 170nm2/sec
>
> >>Let me guess, .64 x 256 = 150 nm^2. Do you have 256 lipids?
>
> >
> > Could you please tell where I have done mistake?
> > Thanks in advance.
>
>
>
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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