[gmx-users] Projection of crystal structure on PCA plot

[Anirban]

Dear Tsjerk,

Thank you very much for the explanation.

So, in other words, as I have carried out PCA on the basis of CA atoms from
the MD trajectory, so if I wish to project the crystal structure onto the
EV, then I need to consider only the CA atoms of the crystal structure
(which in that case won't be the exact crystal structure) as well. Right?

Thanks a lot again.

Regards,

Anirban

On Thu, Jun 6, 2013 at 3:56 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Anirban,
>
> The eigenvectors obtained from the simulation are a way of rewriting the
> coordinates of your structures, not in terms of atoms-XYZ, but as
> combinations of these. Because they are combinations of atom-positions,
> they are defined for the selection of atoms used for the calculation. If
> your crystal structure has the same atoms, which is true if you did not use
> hydrogen atoms, or modeled parts for the covariance analysis, then you can
> project that structure onto the eigenvectors determined, in exactly the way
> you describe in your question.
>
> Hope it helps,
>
> Tsjerk
>
>
>
> On Thu, Jun 6, 2013 at 12:06 PM, Anirban <reach.anirban.ghosh at gmail.com
> >wrote:
>
> > Hi ALL,
> >
> > I have carried out a simulation of a protein and have carried out PCA on
> > the entire trajectory. I have obtained a 2D projection plot of EV1 on
> EV2.
> > Now I want to locate the conformation of the crystal structure (with
> which
> > I started the MD) on this map. How to do this? Can I use "g_anaeig -v
> > Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n Prt_CA.ndx
> > -first 1 -last 2 -2d 2dproj.xvg" to obtain the crystal structure
> position?
> > Or do I need to calculate covariance matrix for the crystal str.(I need a
> > set of them in that case) and then use g_anaeig?
> > Thanks a lot in advance.
> >
> > Regards,
> >
> > Anirban
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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