Did you align your structures first using the RMSD command? I'm assuming
you used ptraj's matrix facilities to calculate your PCA clustering stuff,
yes? From what I recall, I don't think the normal steps in PCA calculations
do a fit automatically, though this is necessary to get "true" principle
components (since you obviously don't care about simple translations and
rotations).
That said, I don't know much about the analysis you're trying to do since
I've never done it myself.
HTH,
Jason
On Wed, Sep 28, 2011 at 7:44 AM, Linda catherine <lindajanaki.gmail.com>wrote:
> Dear friends,
>
> i did PCA clustering for my MD run and the plot ranges from 1-100.
>
> Is it fine as a see very less deviations in all papers showing PCA plots?
>
> Regards
>
> linda
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 28 2011 - 23:00:02 PDT
