Thanks Dan,
I print the covariance matrix to the file and analyze via MATLAB.
On Thu, Dec 17, 2020 at 10:39 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Dec 16, 2020 at 6:54 AM DHEERAJ CHITARA <rs138.iiita.ac.in> wrote:
> >
> > Dear Amber Users,
> >
> > How do I get Top mode contribution from PCA analysis
> > <
> https://amberhub.chpc.utah.edu/introduction-to-principal-component-analysis/
> >
> > for
> > plotting Relative Position Fluctuations.
>
> Assuming you mean you want the RMSF for the eigenvector with the
> largest eigenvalue, use the 'modes' analysis with the 'fluct' keyword
> and use 'beg 1 end 1'; cpptraj sorts the eigenvectors from the largest
> eigenvalue to smallest.
>
> >
> > How do I get individual eigen-values for C-alpha atoms using PCA analysis
> > <
> https://amberhub.chpc.utah.edu/introduction-to-principal-component-analysis/
> >
>
> Calculate the covariance matrix for just the C-alpha atoms (.CA).
>
> See the manual for full details and some examples.
>
> -Dan
>
> > ?
> >
> > --
> > Dheeraj
> > _______________________________________________
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>
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--
----
Dheeraj Chitara
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Received on Thu Dec 17 2020 - 23:00:02 PST
