[gmx-users] question about g_sas

[Berk Hess]

>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] question about g_sas
>Date: Mon, 20 Dec 2004 16:54:58 +0100
>
>On Tue, 2004-12-21 at 00:41 +0900, コウ チ wrote:
> > hello:
> >   i used g_sas to plot per resdiue's solvent accessible surface area( 
>the
> > input file is confoug.gro and topol.tpr). the output resarea.xvg file is
> > like :
> > ....
> > #
> > @    title "Area per residue"
> > @    xaxis  label "Residue"
> > @    yaxis  label "Area (nm\S2\N)"
> > @TYPE xy
> >          1           0          0
> >          2   0.0925984     0
> >          3           0          0
> >          4   0.0226195 3.13147e-06
> > .....
> >
> >  if the second column value indicates the area of residue then what is 
>the
> > meaning of the third column value (ie: 3.13147e-06)?
> >  also i  don't know the algorithm of the programme. does it only caclute
> > per residue's solvent accessible area? it seems the result of g_sas tool 
>is
> > different with other sas compute programme.
>did you use CVS version? Otherwise the per residue value is not correct.

The per residue output should be correct in 3.2.0 and 3.2.1.
The values are only incorrect when an index  group is selected which does 
not consist
of all the non-solvent atoms in the systems.

The third column is the standard deviation (fluctuation).

Berk.

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