[gmx-users] what difference between RMSF and RMDEV

[Justin A. Lemkul]

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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     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>
> 
>     ==============================__==========
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/__mailman/listinfo/gmx-users
>     <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>     Please search the archive at
>     http://www.gromacs.org/__Support/Mailing_Lists/Search
>     <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>     <http://www.gromacs.org/Support/Mailing_Lists>
> 
> 
> 
> 
> -- 
> 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

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