ahmet yıldırım wrote:
Dear Justin,
Thanks for your reply.
Tsjerk:
http://lists.gromacs.org/pipermail/gmx-users/2009-October/045884.html
There are two things to distinguish:
1. The reference structure used to remove translational and
rotational
degrees of freedom
2. The reference against which the deviations (on a per atom
base) are
calculated that are then squared, averaged and taken the root of
(root
mean square fluctuation).
These two need not be the same. It is common, and most sensible, to
calculate the deviations against the average structure, after
fitting
all structures in the trajectory against a certain reference
structure. With option -od the deviations against the reference used
for fitting are calculated rather than against the average. You do
need a reference for fitting, since otherwise you include overall
rotation and translation in the calculation of the RMSF, which you
usually wouldn't want.
1.) For RMSD, You said (i.e. the one present in the .tpr file). which
one? How do Gromacs select the reference structure?
You provide g_rmsf with a .tpr file. It contains coordinates, which Gromacs
then uses as the reference structure.
2.) Tsjerk: RMSF calculate the deviations against the average structure,
after fitting all structures in the trajectory against a certain
reference structure.
the reference structure is taken as average over the trajectory. That
is, it is the average structure (please look at example). isn't it?
_For example:_
coordinates of N atom:
x y z
2 4 6
8 7 1
8 1 2
the average structure of N atom:[(x1+x2+x3)/3, (y1+y2+y3)/3,
(z1+z2+z3)/3]. isnt it?
x y z
6 4 3
3.) This "The reference structure used to remove translational and
rotational degrees of freedom" is RMSD???
This question does not make sense to me. A least squares fit is done on the
trajectory against the reference structure to remove the effects of global
rotation and translation. From this fitted trajectory, the desired quantities
are calculated.
-Justin
2011/9/21 Justin A. Lemkul <[email protected] <mailto:[email protected]>>
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 <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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--
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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