[gmx-users] problem about g_sas of POPC bilayer

[David van der Spoel]

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 
> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/2135081_2127495/2135237/1?PARTNER=3&OAS_QUERY=null>
> 
> 
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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