[gmx-users] g_covar

[Yuri Garmay]

I know, but the best reference is "mean". And it is another mean that
calculated after fit at some frame.

2011/8/16 Tsjerk Wassenaar <tsjerkw at gmail.com>

> Hi,
>
> > This questuion may be hard. You need rabbi's advice))
> > But there are some feature of the reference structure that makes it good
> or
> > bad. It is mean deviation of the atomic coordinates of the fited
> structures
> > from the reference, the best reference minimizes this measure. For a
> rigid
> > structure it is acceptable choice to use first or any other frame, but
> for a
> > flexible it can produce misfit and tangible distortion of the
> conformations'
> > relations.
>
> The reference is used to align the system, not to calculate the
> deviations, unless explicitly specified to do so, which usually does
> not make sense. I've commented on that on the list on several
> occasions. Taking the first frame, or the last or another is all fine.
> Just as long as the same reference is used for all trajectories that
> are to be compared.
>
> Cheers,
>
> Tsjerk
>
> >
> > Yuri.
> >
> > --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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