Hi Tsjerk, Here's the command line:
minVar -s backbone.pdb -f backbone.xtc -log minVar_method3 -out backbone_minVar+NN.xtc -method 3 -NN 80 -nt_iter 8 -nt 8 -cycle_num 100 -mwa Thomas On 17 June 2013 23:37, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hey Thomas, > > No, there is no such tool. Sorry. > May I ask how you did the MinVar fitting? > > Cheers, > > Tsjerk > > > > On Mon, Jun 17, 2013 at 12:55 PM, Thomas Evangelidis <teva...@gmail.com > >wrote: > > > Dear GROMACS list, > > > > I used minVar to remove global rotations and translations from a > > trajectory, but due to memory issues I used a replica with only the > > backbone of the protein. Now I want to fit each frame of the original > > protein trajectory to the respective frame of the processed backbone > > trajectory. Is there any GMX tool that can do that? > > > > thanks, > > Thomas > > > > > > > > -- > > > > ====================================================================== > > > > Thomas Evangelidis > > > > PhD student > > University of Athens > > Faculty of Pharmacy > > Department of Pharmaceutical Chemistry > > Panepistimioupoli-Zografou > > 157 71 Athens > > GREECE > > > > email: tev...@pharm.uoa.gr > > > > teva...@gmail.com > > > > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > -- > > 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. > -- > 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 > -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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