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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?

Thanks!

Qiao Xue

_______________________________________________

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AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

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

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?

Thanks!

Qiao Xue

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

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

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