<P>
<BR>
Thanks for your reply<BR>
NO, I am having 64 lipids in each leaflet of bilayer. <BR>
I want to calculate average area per lipid. what I have mentioned options are correct for g_sas?<BR>
Thanks for your appreciation<BR>
<BR>
innale wrote:<BR>
> Hi all,<BR>
> I have downloaded POPC bilayer from peter teileman,s website and <BR>
> simulated for 5ns under anisotropic pressure coupling. When I drew a <BR>
> potential energy plot its shown that system is stabilised, so I have <BR>
> stopped the simulation at 5ns.<BR>
> After that I have mentioned g_sas command for calculating surface area <BR>
> of lipid in this way and got .xvg file like below mentioned<BR>
> <BR>
> command : g_sas -f 5ns_popc.xtc -s min_popc.tpr -pbc -o area_popc.xvg<BR>
> <BR>
> .xvg File:<BR>
> @ title "Solvent Accessible Surface"<BR>
> @ xaxis label "Time (ps)"<BR>
> @ yaxis label "Area (nm\S2\N)"<BR>
> @TYPE xy<BR>
> @ view 0.15, 0.15, 0.75, 0.85<BR>
> @ legend on<BR>
> @ legend box on<BR>
> @ legend loctype view<BR>
> @ legend 0.78, 0.8<BR>
> @ legend length 2<BR>
> @ s0 legend "Hydrophobic"<BR>
> @ s1 legend "Hydrophilic"<BR>
> @ s2 legend "Total"<BR>
> @ s3 legend "D Gsolv"<BR>
> 0 152.383 228.165 380.548 0<BR>
> 0.2 149.279 230.277 379.555 0<BR>
> 0.4 153.175 229.306 382.481 0<BR>
> 0.6 149.312 229.188 378.499 0<BR>
> 0.8 149.708 228.811 378.518 0<BR>
> 1 149.972 229.69 379.662 0<BR>
> 1.2 155.587 229.615 385.202 0<BR>
> 1.4 151.953 227.696 379.649 0<BR>
> 1.6 149.113 229.903 379.016 0<BR>
> 1.8 151.062 227.394 378.456 0<BR>
> 2 149.278 226.934 376.213 0<BR>
> 2.2 151.095 225.68 376.774 0<BR>
> 2.4 149.873 229.576 379.449 0<BR>
> 2.6 148.387 230.391 378.778 0<BR>
> 2.8 147.627 227.792 375.419 0<BR>
> 3 148.156 229.589 377.745 0<BR>
> 3.2 145.051 229.568 374.619 0<BR>
> 3.4 147.231 229.814 377.044 0<BR>
> 3.6 145.348 229.392 374.741 0<BR>
> 3.8 148.717 229.43 378.146 0<BR>
> 4 153.307 230.834 384.142 0<BR>
> 4.2 153.604 230.6 384.204 0<BR>
> 4.4 154.397 229.345 383.742 0<BR>
> 4.6 155.718 230.864 386.582 0<BR>
> 4.8 155.685 231.226 386.911 0<BR>
> 5 152.911 231.332 384.243 0<BR>
> 5.2 153.935 229.453 383.388 0<BR>
> 5.4 154.43 231.396 385.826 0<BR>
> . <BR>
> .<BR>
> .<BR>
> .<BR>
> .<BR>
> till 5000ps.<BR>
> <BR>
> I have searched in gmx-archives about SAS of lipid, I found that lipid <BR>
> SAS should be 0.64 nm^2/sec but I got values range from 150 to 170nm2/sec<BR>
<BR>
>>Let me guess, .64 x 256 = 150 nm^2. Do you have 256 lipids?<BR>
<BR>
> <BR>
> Could you please tell where I have done mistake?<BR>
> Thanks in advance.
</P>
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