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
