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 <tsje...@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. > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > 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@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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