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

[Qasim Pars]

Dear Tsjerk,

Then my plot is not strange?
You said that "The overall mean of any set of projections lies at the
origin". Could you please suggest me any material that explains what you
said? I couldn't find anything about that on google.

Cheers,

On 7 June 2016 at 15:15, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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.
> --
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-- 
Qasim Pars