yuri.from.spb at gmail.com
Tue Aug 16 11:16:08 CEST 2011
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>
> > This questuion may be hard. You need rabbi's advice))
> > But there are some feature of the reference structure that makes it good
> > bad. It is mean deviation of the atomic coordinates of the fited
> > from the reference, the best reference minimizes this measure. For a
> > 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
> > 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.
> > 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
> gmx-users mailing list gmx-users at gromacs.org
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