Right :) Cheers,
Tsjerk On Mon, Oct 5, 2015 at 11:07 PM, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > Thanks for the clarification Tsjerk. So my previous assumption was right. > Basically if I want to align on the backbone but want the RMSF of Calpha I > need to align first, save the trajectory and do RMSF with -nofit right? > > Max > > > On Oct 5, 2015, at 4:54 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > > > > Hi Ebert, > > > > Use C-alpha as the group. Yes, it will be used for fitting and > calculation > > of the RMSF. > > > > Cheers, > > > > Tsjerk > > On Oct 5, 2015 22:44, "Ebert Maximilian" <m.eb...@umontreal.ca> wrote: > > > >> Oh infact no thats not the case it is still the RMSF of all atoms in the > >> residue. So back to my initial question. How can I calculate the RMSF on > >> the Ca of each residue? > >> > >> Sorry if this caused any confusion. > >> > >> Max > >> > >>> On Oct 5, 2015, at 4:36 PM, Ebert Maximilian <m.eb...@umontreal.ca> > >> wrote: > >>> > >>> I think I can answer my own question again. The group you use for root > >> mean square calculation is also the RMSF group. If the group has more > than > >> one atom per residue and I use -res I get the average RMSF of all atoms > per > >> residue. > >>> > >>> Hope this is correct. > >>> > >>> Max > >>> > >>>> On Oct 5, 2015, at 2:46 PM, Ebert Maximilian <m.eb...@umontreal.ca> > >> wrote: > >>>> > >>>> Hi there, > >>>> > >>>> I want to calculate ht RMSF of the carbon alpha. First which atoms are > >> used if I calculate the RMSF per residue with -res and how can I > calculate > >> the RMSF of carbon alpha or NH vector etc? Can’t seem to find an input > >> except for the group of the alignment for the -fit > >>>> > >>>> Thank you, > >>>> > >>>> Max > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe requests visit > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >>> > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.