Re: [AMBER] Top Mode Contribution in PCA Analysis.

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 17 Dec 2020 12:08:46 -0500

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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Received on Thu Dec 17 2020 - 09:30:03 PST