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