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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 6 12:26:26 CEST 2013

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,


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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