[gmx-users] Re: gmx-users Digest, Vol 45, Issue 30

[Tsjerk Wassenaar]

Hi Prasad,

You also have to reckon that the RMSD is always positive, so the average
RMSD will also always be positive. It's a chi-variate.
Try some thought experiments with distances, average distances and distances
to an average position.

Cheers,

Tsjerk

On Jan 10, 2008 8:09 PM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> Prasad Gajula wrote:
> > Dear Dr. David,
> > Thank you very for the reply.
> > When i looked the energy minimized average structure it looks just fine.
> > ??
> but you did not say energy minimized... check the rmsd between average
> and minimized average structure as well.
>
> Maybe you want to do a clustering analysis instead?
> >
> >
> >>> I calcualted the average structure from the simulation trajectory.
> when
> >>> I
> >>> calculate the rmsd of the protein to this average sturture, it is
> giving
> >>> average rmsd of 0.16 nm. But, it is not clear for me why the average
> >>> sturcture is never adapted rmsd near (or equal) to zero. I did not
> >>> calculate the rmsd with respect to the starting structure either.
> >>> Any clue?
> >> the average structure is unphysical, it may have long bonds etc.
> >>
> >
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>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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