Hi, Fitting is commonly done mass weighted if the reference file contains masses, like a run input file. But covariance analysis is only performed mass weighted if explicitly requested (and masses are available). If mass-weighted analysis is not requested, the masses for the fit will all be set to one, so as to assure that the fit and the analysis will concern the same thing. That is what the message is trying to tell. So no problem (unless you wanted mass-weighted analysis).
Hope it helps, Tsjerk On Tue, Jun 1, 2010 at 8:51 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > > > ----- Original Message ----- > From: pawan raghav <pwnr...@gmail.com> > Date: Wednesday, June 2, 2010 4:18 > Subject: [gmx-users] g_covar > To: gmx-users@gromacs.org > >> Thanks Mark for your advice >> >> Note: The fit analysis group are identical, while the fit is mass weighted >> and the analysis is not making the fit non mass weighted. >> >> But, this is the the real unning out put of the command prompt > > No, it isn't. :-) I've now consulted the 4.0.7 source code, this message > would have had a full stop and a capital M. Since they were missing, it > looked like you were saying something confused. > > g_covar won't do a mass-weighted fit with a non-mass-weighted analysis. > g_covar -h talks about this. > >> Please let me know anyone what is the meaning of this note? and also tell >> me is it right to choose C-alpha group for two times? > > >> Yes I want to do the structure-fitting on the same set of atoms as I do >> the analysis. > > Well, then you need to make a choice consistent with that. > > Mark > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology 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/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/mailing_lists/users.php
