[gmx-users] Calculations of area per lipid using g_sas
David van der Spoel
spoel at xray.bmc.uu.se
Mon Jul 9 09:11:15 CEST 2007
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
> 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
this is why we do dynamics. we like fluctuations.
> Thanks for your help in advance.
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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
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