[gmx-users] what difference between RMSF and RMDEV

[ahmet yıldırım]

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?

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???


2011/9/21 Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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-- 
Ahmet YILDIRIM
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