Hi Nawel, The reference distances are computed from the reference structure provided with the option -s.
Cheers, Tsjerk On Mon, Jun 3, 2013 at 12:39 PM, Nawel Mele <nawel.m...@gmail.com> wrote: > Hi, > > THanks for your answers. > Just for be sure, with g_rmsdit the reference structure correspond to the > frame at time 0?? > Because in the manual the rmsd equation show that reference structure > correspond to the time t=0 but the help doesn't confirm. > > THanks a lot for your help, > > > > 2013/6/2 Tsjerk Wassenaar <tsje...@gmail.com> > > > Hi Nawel, > > > > g_rmsdist calculates the RMSD of distances, and distances are invariant > to > > translation and rotation. > > > > Cheers, > > > > Tsjerk > > > > > > On Sun, Jun 2, 2013 at 1:45 PM, Nawel Mele <nawel.m...@gmail.com> wrote: > > > > > Hi, > > > > > > THanks for your answers. I already seen the help for this command but > > when > > > its write > > > "g_rmsdist computes the root mean square deviation of atom distances, > > which > > > has the advantage that* no fit is needed* like in standard RMS > deviation > > as > > > computed by g_rms" what mean excatly "no fit is needed"?? > > > Because when you compute a RMSD calculation its necessary to align the > > > structure so I am a bit confused when its write "no fit is needed". > > > Fit is processed directly by the command? > > > > > > I am sorry I am little confused. > > > > > > THanks a lot > > > > > > > > > 2013/6/2 Mark Abraham <mark.j.abra...@gmail.com> > > > > > > > See g_rmsdist -h > > > > > > > > Mark > > > > > > > > > > > > On Sun, Jun 2, 2013 at 12:29 PM, Nawel Mele <nawel.m...@gmail.com> > > > wrote: > > > > > > > > > Hello everyone. > > > > > > > > > > During the calculation of the rms with g_rmsdist command , the > > > reference > > > > > and the current structure are aligned before calculating?? > > > > > > > > > > Regards, > > > > > > > > > > > > > > > -- > > > > > *Mlle* Mele Nawel > > > > > Master 2 In Silico Drug Design > > > > > University of Paris Diderot/Strasbourg > > > > > -- > > > > > 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 > > > > > > > > > -- > > > > 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 > > > > > > > > > > > > > > > > -- > > > *Mlle* Mele Nawel > > > Master 2 In Silico Drug Design > > > University of Paris Diderot/Strasbourg > > > -- > > > 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 > > > > > > -- > *Mlle* Mele Nawel > Master 2 In Silico Drug Design > University of Paris Diderot/Strasbourg > -- > 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