[gmx-users] structure alignement :g_rmsdist

[Nawel Mele]

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