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

[Hwankyu Lee]

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 <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Re: Calculations of area per lipid using
        g_sas
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <46931F51.3070905 at anu.edu.au>
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