Dear Mark and David,
Thanks for your reply. Dimension of 128-lipid bilayer system is
6.32x6.43x8.57nm, which leads to the projected area/lipid of ~63.5 A^2,
and the box size is consistent during whole simulation time. In order
to measure total SASA, I typed "g_sas -f **.xtc -s **.tpr -o **.xvg
-solsize **" with different values of -solsize. Outputs are shown
below. Here, my questions is 1) With bigger solvent probes, why does
the total SASA decrease ? I thought that SASA should increase because
bigger solvents will not insert into the lipid headgroups.
2) with -solsize 1.9, area/lipid can be obtained from 43.0275/2/64=33.6
A^2. How can this be smaller than the projected area/lipid, ~63.5 ?
For -solsize 1.5, -----------------------------
# This file was created Tue Jul 10 10:25:24 2007
# by the following command:
# g_sas -f test.xtc -s md.tpr -o area0.xvg -solsize 1.5 -b 100000 -e 200000
#
# g_sas is part of G R O M A C S:
#
# Gnomes, ROck Monsters And Chili Sauce
#
@ title "Solvent Accessible Surface"
@ xaxis label "Time (ps)"
@ yaxis label "Area (nm\S2\N)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrophobic"
@ s1 legend "Hydrophilic"
@ s2 legend "Total"
@ s3 legend "D Gsolv"
100000 0 85.8878 85.8878 0
100050 0 88.9415 88.9415 0
100100 0 88.0002 88.0002 0
-----------------------------------------------
For, -solsize 1.7,
-----------------------------------------------
# This file was created Tue Jul 10 10:27:27 2007
# by the following command:
# g_sas -f test.xtc -s md.tpr -o area1.xvg -solsize 1.7 -b 100000 -e 200000
#
# g_sas is part of G R O M A C S:
#
# GRowing Old MAkes el Chrono Sweat
#
@ title "Solvent Accessible Surface"
@ xaxis label "Time (ps)"
@ yaxis label "Area (nm\S2\N)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrophobic"
@ s1 legend "Hydrophilic"
@ s2 legend "Total"
@ s3 legend "D Gsolv"
100000 0 82.7674 82.7674 0
100050 0 84.0109 84.0109 0
100100 0 85.2114 85.2114 0
-----------------------------------------
For -solsize 1.9
-----------------------------------------
This file was created Tue Jul 10 10:28:40 2007
# by the following command:
# g_sas -f test.xtc -s md.tpr -o area2.xvg -solsize 1.9 -b 100000 -e 200000
#
# g_sas is part of G R O M A C S:
#
# Good gRace! Old Maple Actually Chews Slate
#
@ title "Solvent Accessible Surface"
@ xaxis label "Time (ps)"
@ yaxis label "Area (nm\S2\N)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrophobic"
@ s1 legend "Hydrophilic"
@ s2 legend "Total"
@ s3 legend "D Gsolv"
100000 0 43.0275 43.0275 0
100050 0 47.978 47.978 0
100100 0 38.3633 38.3633 0
----------------------------------------------
Thanks,
best,
Hwankyu.
Message: 5
Date: Tue, 10 Jul 2007 15:55:29 +1000
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Re: Calculations of area per lipid using
g_sas
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hwankyu Lee wrote:
[Hide Quoted Text]
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?
Show us your box dimensions at a point when you observe this to occur -
or preferably a relevant chunk of both g_sas and g_energy output.
Mark
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