[gmx-users] least-squares fitting the second structure on the reference structure

[Mark Abraham]

Hi,

Each frame of the trajectory is fitted to the reference structure
independently of the others... but not if you're using gmx confrms, which
only acts on a single frame anyway...

Mark

On Thu, Jun 23, 2016 at 12:11 AM Qasim Pars <qasimpars at gmail.com> wrote:

> Hi Tsjerk,
>
> Thanks, I know that. I was wondering how does a second structure (for
> instance third frame) fit mathematically onto the reference structure? I
> understand the least-square fitting for only one data set but I couldn't
> understand the the least-square fitting for two data sets that fit on each
> other's.
>
> Cheers,
>
> On 23 June 2016 at 00:14, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> > Hi Qasim,
> >
> > If you fit a trajectory, with trjconv -fit rot+trans, then each frame is
> > fit onto the reference.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Tue, Jun 21, 2016 at 11:12 AM, Qasim Pars <qasimpars at gmail.com>
> wrote:
> >
> > > Dear users,
> > >
> > > From GROMACS online manual:
> > > gmx confrms computes the root mean square deviation (RMSD) of two
> > > structures after least-squares fitting the second structure on the
> first
> > > one.
> > >
> > > My question is how GROMACS does least-squares fitting the second
> > structure
> > > (each frame of trajectory) on the first one (reference structure)? It
> > > calculates the least-squares fitting of the second structure and the
> > first
> > > one seperately?
> > >
> > > Thanks for your helps.
> > > --
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> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
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>
>
> --
> Qasim Pars
> --
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