VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 20 2006 - 16:13:57 CDT

Arturas,
  No, not like Gromacs. The 'measure rmsf' command assumes
that you've alredy done the fitting (as with 'measure rmsd').
No, the rmsf for each atom is calculated independently. If you want
all atoms in a group, you'll want to use 'measure rmsd' and provide
an appropriate group selection instead.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 20, 2006 at 08:33:32PM +0000, ziemys_at_ecr6.ohio-state.edu wrote:
> HI,
>
> Is RMSF in VMD computed as in GROMACS (the root mean square standard deviation of atomic positions after first fitting to a reference frame) ?
>
> What frame is the reference for fitting (if RMSF calculated like in GROMACS) ?
>
> Will the average computed RMSF of all atoms in a residue be the same as a group RMSF ?
>
> With best
> Arturas
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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