[gmx-users] g_rmsf -res yes ? => should I type "yes" to activate the "average-function" ?

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> 
> 
> Hi
> 
> g_rmsf -res yes ?
> 
> g_rmsf -res no ?
> 
> 
> should I type "yes" to activate the "average-function"? 
> 

No.  The command is either g_rmsf or g_rmsf -res.  There is no "yes" or "no" 
required.

> 
> As i tested "g_rmsf -res",
> the average is not over time and not over the atoms in the residue.
> 

You will not get a plot over time.  The calculation is done over time, but only 
the final result is plotted.  If you have a plot of RMSF vs. residue, then 
averaging has been done over all the frames supplied, and over all the atoms in 
each residue.  Unless you can prove that something has not been done correctly, 
then there is no need to repeatedly post the same question.

-Justin

> Anyway, how to activate the "average function" ?
> Thank you
> Lin
> 
> 
> 
> Chih-Ying Lin wrote:
>  >
>  >
>  >
>  >
>  > Hi
>  > g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg
>  >
>  >  From manual => it says   " Calculate averages for each residue  "
>  >                      =>  does Gromacs do average over time for each
>  > residue ?
> 
> The average is done over time and over the atoms in the residue.
> 
>  >                      => however, the results did not show difference
>  > with and without " -res  "
>  >
> 
> I doubt that.  Without -res, you get RMSF per atom.  With -res, you get 
> RMSF per
> residue.  The output is inherently (and necessarily) different.
> 
> -Justin
> 
>  >
>  >
>  >
>  >
>  >
>  > Thank you
>  > Lin
>  >
> 

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

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

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