[gmx-users] structure alignement :g_rmsdist

[Tsjerk Wassenaar]

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.mele at 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 <tsjerkw at 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.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
> > > > > --
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> > > --
> > > *Mlle* Mele Nawel
> > > Master 2 In Silico Drug Design
> > > University of Paris Diderot/Strasbourg
> > > --
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> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
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>
>
> --
> *Mlle* Mele Nawel
> Master 2 In Silico Drug Design
> University of Paris Diderot/Strasbourg
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.