[gmx-users] what difference between RMSF and RMDEV
Justin A. Lemkul
jalemkul at vt.edu
Wed Sep 21 19:34:03 CEST 2011
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
========================================
More information about the gromacs.org_gmx-users
mailing list