[gmx-users] what difference between RMSF and RMDEV

[Justin A. Lemkul]

ahmet yıldırım wrote:
> Dear users,
> 
> g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res
> 
> With the option -od the root mean square deviation with respect to the 
> reference structure is calculated.
> Then,
> RMSDEV is the RMSD per residue (the root mean square deviation with 
> respect to the reference structure is calculated).
> 
> and
> RMSF is the RMSD per residue (the root mean square fluctuation (RMSF, 
> i.e. standard deviation) of atomic positions after (optionally) fitting 
> to a reference frame). That is, it is the measurement averaged over all 
> atoms in each residue.
> 
> Now what difference?
> 

The RMSD is measured relative to the reference structure (i.e. the one present 
in the .tpr file).  RMSF is measured with respect to average coordinates.

-Justin

> I am confused.
> 
> -- 
> Ahmet YILDIRIM
> 

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

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

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