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

[Tsjerk Wassenaar]

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.