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

[Hwankyu Lee]

Dear Mark,

I just measured the projected XY-area (simply XY-size of box), and used 
typical periodic boundary condition (In g_sas, default considers PBC). 
In the small system (128 lipid bilayer), there is no undulation, so 
projected area per lipid may be almost the same as non-projected area 
per lipid.  So, total solvent accessible surface area (the third 
column) should be always larger than the projected XY-area, but I 
observed that total SASA become smaller than the projected XY-area at 
some point. Could you give me some suggestions?

best,
Hwankyu.


Date: Mon, 9 Jul 2007 10:23:46 +1000 (EST)
From: "Mark Abraham" <mark.abraham at anu.edu.au>
Subject: Re: [gmx-users] Calculations of area per lipid using g_sas
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
        <58659.150.203.145.27.1183940626.squirrel at sqmail.anu.edu.au>
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> 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