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

[Mark Abraham]

> 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?

How are you measuring XY-area? What periodicity are you using?

> 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?
>
> 3) I saw SASA fluctuate quite a lot. Is there any way to decrease
> fluctuation?

Fluctuating with what?

Mark