[gmx-users] how to obtain error bar for plotting?

[Mark Abraham]

On 12/24/2011 10:40 PM, leila karami wrote:
> Dear gromacs users
>
> I would like to calculate the standard deviation (as the error bar) 
> for rmsd.xvg file.
>
> If rmsd.xvg was used in excel software, it gives a graph as rmsd vs 
> time. I want to have a file containing rmsd vs time
>
> and error bar relating to rmsd values such that after plotting by 
> excel it give rmsd vs time and error bar.

The RMS deviation in atomic coordinates between a reference and other 
state is an exact quantity. There's no statistical error to plot.

Mark

>
> I have tried using g_analyze:
>
> In this tool, is -av mandatory?
>
> g_analyze -av average.xvg -errbar stddev -f rmsd.xvg
>
> It gives me only a average.xvg file and at the end
>
>
>                                                                       
> std. dev.                   relative deviation of
>                                          standard                
> ---------                cumulants from those of
> set         average              deviation               
> sqrt(n-1)               a Gaussian distribition
>                                                                        
>                                 cum. 3   cum. 4
> SS1    3.215937e-01     5.472631e-02       7.739468e-04             
> -0.296    0.083
>
>
> how to access error bar values?
>
> any help will highly appreciated.
>
>


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