[gmx-users] problem about g_sas of POPC bilayer

minnale minnale_gnos at rediffmail.com
Fri Jun 6 08:14:26 CEST 2008


 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 

Could you please tell where I have done mistake?
Thanks in advance.
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