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

[Anirban]

Thanks a lot Tsjerk :)

-Anirban

On Thu, Jun 6, 2013 at 4:42 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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.
> --
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