minnale 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.
Maruti
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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