[gmx-users] Calculations of area per lipid using g_sas

[David van der Spoel]

Hwankyu Lee wrote:
> Dear GMX users,
> 
> I'm interested in calculating non-projected area/lipid of huge bilayer 
> with undulations. I think that if the bigger solvent probes were used, 
> the non-projected area per lipid may be reasonably calculated from the 
> solvent accessible surface area because solvent probes cannot be 
> inserted between lipid headgroups, which will avoid overestimation of 
> area per lipid.  So, I'm testing this with small bilayer (128 lipids) 
> using g_sas, and have some questions.
> 
> 1) If the bigger solvent probes (such as -solsize 1.7 or so) are used, 
> SASA of lipid will become smaller, but should be always bigger than the 
> XY-area of this small bilayer system.  But, when I increased the value 
> of -solsize, SASA becomes even smaller than the XY-area at some point. 
> In this case, how can SASA be smaller than XY-area of the bilayer?
there are three curves in the file, hydrophobic, hydrophilic and total. 
Total should be larger than the area, but hydrophobic, the first, not 
necessarily.
> 
> 2) The manual says that -ndots is related to accuracy, but when I tried 
> different values, I don't see trends of increase or decrease.  Could you 
> tell me what it is and what the reasonable value will be?
default is probably good enough.
> 
> 3) I saw SASA fluctuate quite a lot. Is there any way to decrease 
> fluctuation?
this is why we do dynamics. we like fluctuations.

> 
> Thanks for your help in advance.
> 
> best,
> Hwankyu.
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-- 
David van der Spoel, Ph.D.
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