[AMBER] some questions about PCA

From: qiao xue <xueqiaoup.gmail.com>
Date: Tue, 3 Sep 2013 10:55:35 +0800

Dear Amber Users:
    I have some problems when performing PCA. The follows is the script:

trajin md1.mdcrd
rms previous .CA,C,N time 2
matrix covar .CA name cvmat out cvmat.dat
analyze matrix cvmat name evecs out evecs.dat vecs 25
projection modes evecs .CA out project.dat beg 1 end 2

    The first question is: How could I know the total variance? I know
the largest eigenvalue, but I do not know the total variance. So I
could not get the ratio. And I do not know whether PC1 and PC2 can
explain the motion of the system.
    The second question is: When I get the projection data. I found
that the data has big difference with any tutorials and literatures.
In tutorials, when ploting the datas into scatter diagram (X axis:PC1;
Y axis: PC2), the range of x and y axises are -2 nm to 2 nm. However,
in my scatter diagram, the range of the datas varied from -300 to 300.
And I do not know the unit of measurement. How could I get the correct
projection datas?
   The last question is: I have N atoms to calculate. But the
covariance matrix dimension is 3N * 3N, this can not be used as the x,
y axis. How could I get the N * N covariance matrix?

                                            Qiao Xue

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Received on Mon Sep 02 2013 - 20:00:03 PDT
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