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

[Qasim Pars]

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