[gmx-users] (no subject)

[Justin A. Lemkul]

Anitha wrote:
> my header starts as
> 
> # g_sas is part of G R O M A C S:
> #
> # GROtesk MACabre and Sinister
> #
> @    title "Area per residue"
> @    xaxis  label "Residue"
> @    yaxis  label "Area (nm\S2\N)"
> @TYPE xy
>          1    0.846565   0.312334
>          2       0.598   0.189911
>          3    0.837035   0.363443
>          4     1.14936   0.304359
>          5    0.630063   0.233607
>          6    0.625571   0.321569
>          7    0.261401   0.240533
>          8   0.0940011  0.0872611
> 
> 
> i`m not able to understand what the second and third column represents....
>         

This is a plot of surface area per residue, and as the y-axis label indicates, 
you have area in square nm.  The second column is the area, the third column is 
the fluctuation.  The last column is not immediately obvious, but from the code 
it is clear (and an identical question posted to this list not too long ago).

-Justin

> 
> 
> On Fri, Jul 30, 2010 at 4:33 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Anitha wrote:
> 
>         In the headers file also i didn`t get the answer about those
>         lines....
> 
> 
>     Well, what do they say?
> 
>     -Justin
> 
>         On Fri, Jul 30, 2010 at 4:01 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>            Anitha wrote:
> 
>                I executed the following command.
> 
>                g_sas -s topol.tpr -f traj.xtc -or resarea.xvg -o area.xvg
>                xmgrace -nxy resarea.xvg
> 
> 
>                I have chosen the protein group for surface calculation
>         and output.
>                I get two sets of values: one is bigger (black) than the
>         other
>                (red).
> 
>                I have checked the manual and other sources, but I could
>         not find an
>                answer about the black and red line.  What does red and black
>                line shows?
> 
> 
>            Read the headers of the .xvg file.
> 
>            -Justin
> 
> 
>                --         S.Anitha
> 
> 
>            --     ========================================
> 
>            Justin A. Lemkul
>            Ph.D. Candidate
>            ICTAS Doctoral Scholar
>            MILES-IGERT Trainee
>            Department of Biochemistry
>            Virginia Tech
>            Blacksburg, VA
>            jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>         231-9080
> 
>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
> 
>         -- 
>         S.Anitha
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 
> 
> 
> -- 
> S.Anitha
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================