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

[Tsjerk Wassenaar]

Hi Anirban,

Indeed.

:)

Tsjerk


On Thu, Jun 6, 2013 at 1:11 PM, Anirban <reach.anirban.ghosh at gmail.com>wrote:

> 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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-- 
Tsjerk A. Wassenaar, Ph.D.