[gmx-users] projection on the first two eigenvectors obtained from the concatenated trajectories

[Tsjerk Wassenaar]

Hi Qasim,

What makes you think that they should start at 0,0 ?
The overall mean of any set of projections lies at the origin.
PCA is a pretty powerful and advanced technique, that requires quite a bit
of thinking in the preparation, the execution and the interpretation.
Please do read plenty of tutorial material dealing with it, not only from
the perspective of simulations, but also from the linear algebra view.

Cheers,

Tsjerk

On Tue, Jun 7, 2016 at 2:09 PM, Qasim Pars <qasimpars at gmail.com> wrote:

> Dear gmx users,
>
> I have simulated three systems. The projection of each individual
> trajectory on the first two eigenvectors obtained from the concatenated
> trajectory is strange because each projection should start at (0,0) points
> or near (0,0). Please have a look at the plot
> https://www.dropbox.com/s/3jrlkdwbv4csccq/pca.png?dl=0
>
> Why the projections do not start at (0,0) points or near (0,0)? Can anyone
> of you tell me where I might have made a mistake?
>
> In order to remove jumps across the box of each trajectory I used the gmx
> trjconv -pbc nojump. The other commands are below:
>
> trjcat -f wt.xtc one-ligand.xtc two-ligands.xtc -o merged.xtc -cat
>
> gmx covar -f merged.xtc -s wt.pdb
>
> gmx anaeig -f wt.xtc -s wt.pdb -v eigenvec.trr -2d wt.xvg -first 1 -last 2
> gmx anaeig -f one-ligand.xtc -s wt.pdb -v eigenvec.trr -2d one-ligand.xvg
> -first 1 -last 2
> gmx anaeig -f two-ligands.xtc -s wt.pdb -v eigenvec.trr -2d two-ligands.xvg
> -first 1 -last 2
>
> Cheers,
>
> --
> Qasim Pars
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-- 
Tsjerk A. Wassenaar, Ph.D.