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" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Calculations of area per lipid using g_sas
To: "Discussion list for GROMACS users" <[email protected]>
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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
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