Hi Josh, When fitting, trjconv asks for separate groups for performing the fit and for the output. No need to hack anything. You can make a suitable index file using make_ndx.
Cheers, Tsjerk On Thu, Feb 26, 2009 at 7:47 PM, Joshua Adelman <jadel...@berkeley.edu> wrote: > I am trying to use trjconv to generate a new .xtc file in which all frames > have been aligned based on a subset of atoms (e.g. I have a multi-domain > protein and I want to align the trajectory to one of the domains). Using a > standard .ndx file only outputs the atoms associated with the fitted domain. > I was wondering if there is a straightforward way to do what I describe > without having to hack trjconv? > Looking at the source for do_fit.c it looks like if I were to set the mass > of atoms that I didn't want to use in the alignment to zero, then it might > work, but I am generally trying to avoid having to generate a tpr file since > I'm coming from the pdb/psf world. > Any suggestions would be appreciated. > Josh > > ------------------------------------------------------------------------------------------------------ > Joshua L. Adelman > Biophysics Graduate Group Lab: 510.643.2159 > 218 Wellman Hall Fax: 510.642.7428 > University of California, Berkeley http://nature.berkeley.edu/~jadelman > Berkeley, CA 94720 USA jadel...@berkeley.edu > ------------------------------------------------------------------------------------------------------ > > > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://www.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. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
