Thanks for the explanation Daniel, it clears my doubts.
I figured out the modes commands for the fraction of the eigen values also.
On Sun, Jun 5, 2016 at 11:28 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Sat, Jun 4, 2016 at 7:14 AM, Himanshu Joshi <himanshuphy87.gmail.com>
> wrote:
> > Hello folks,
> > I am following the tutorial by Cheatham et al at AMBER15 work shop at
> > London to perform PCA of a structure in MD simulation.
> > http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/
> >
> > I extracted the eigenmode data file from the covariance matrix of
> > coordinates followed by the projection of the structure along the few
> > principle components (PC) using the "projection" command as described in
> > the in above tutorial. If I understand it correctly, it is the dot
> product
> > of the eigen vector and the coordinates of this frame in Angstrom. Please
> > correct me if it is not true.
>
> It's true.
>
> > What does it means that the coordinates
> > "match well" with the PC. What the relatively high projection to one
> > particular mode reflects, some description would be really helpful.
>
> I believe you are referring to this sentence:
>
> 'We can now project the trajectory coordinates along PCs to see how
> much the coordinates of each frame "match up" along each principal
> component.'
>
> Perhaps not the best description - all this means is that when you
> project coordinates along an eigenvector you're getting a sense for
> how far each set of coordinates (i.e. each coordinate frame) has
> "traveled along" that eigenvector (maybe that's not the best
> explanation either). A "high" projection just means the coordinates
> have traveled quite far along that eigenvector. Remember, the
> eigenvectors are just defining new coordinate axes for the movement of
> atoms. They don't necessarily describe actual paths the atoms take
> during the simulation.
>
> >
> > My other question is how do I know how much does the corresponding PC
> > contribute to the total motion.
>
> Check out the 'modes eigenval' analysis command in cpptraj.
>
> -Dan
>
> >
> > Thank you in advance.
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
--
With Regards
Himanshu Joshi
Department of Physics
IISc Bangalore India
560012
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Received on Sun Jun 05 2016 - 11:30:03 PDT
