[gmx-users] Re: Calculations of area per lipid using g_sas
leehk at umich.edu
Mon Jul 9 20:20:44 CEST 2007
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?
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>
<586126.96.36.199.27.1183940626.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
Fluctuating with what?
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