[gmx-users] structure alignement :g_rmsdist

[Tsjerk Wassenaar]

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.mele at 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.abraham at gmail.com>
>
> > See g_rmsdist -h
> >
> > Mark
> >
> >
> > On Sun, Jun 2, 2013 at 12:29 PM, Nawel Mele <nawel.mele at 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 at 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-request at gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > --
> > gmx-users mailing list    gmx-users at 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-request at 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 at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.