[gmx-users] structure alignement :g_rmsdist

[Nawel Mele]

Thanks, the tpr file using by -s option contains the starting structure of
the simulation so the reference structure correspond to the first structure.

Thanks a lot ,



2013/6/3 Tsjerk Wassenaar <tsjerkw at gmail.com>

> 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.
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-- 
*Mlle* Mele Nawel
Master 2 In Silico Drug Design
University of Paris Diderot/Strasbourg