- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Muthukumaran R <kumaran.bicpu.edu.in>

Date: Sun, 25 Jan 2015 21:12:40 +0530

Dear Amber users,

I am performing PCA calculations using cpptraj in ambertools 14.

There are 630 C-alpha atoms in my protein and the mass-weighted covariance

matrix is 1890 x 1890.

I extracted the eigenvalues and the first 5 are given below.

1 0.48444

2 0.58309

3 1.08605

4 1.58621

5 1.98272

I want to calculate the percentage of variance for each eigenvector.

According to the suggestions given in the mailing list, I understand that

these are frequencies and should be converted to eigenvalues for

calculating variance.

I tried to convert them using the conversion formula,

Freq = 108.587 * sqrt( 0.6 / Eigenvalue )

(http://archive.ambermd.org/201307/0678.html)

But, the first frequency gave a very small eigenvalue (in the range of e-06)

Am I proceeding in the right direction?

I need your valuable suggestions in calculating the percentage variance of

each eigenvector.

Thanks in advance..

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Sun Jan 25 2015 - 08:00:03 PST

Date: Sun, 25 Jan 2015 21:12:40 +0530

Dear Amber users,

I am performing PCA calculations using cpptraj in ambertools 14.

There are 630 C-alpha atoms in my protein and the mass-weighted covariance

matrix is 1890 x 1890.

I extracted the eigenvalues and the first 5 are given below.

1 0.48444

2 0.58309

3 1.08605

4 1.58621

5 1.98272

I want to calculate the percentage of variance for each eigenvector.

According to the suggestions given in the mailing list, I understand that

these are frequencies and should be converted to eigenvalues for

calculating variance.

I tried to convert them using the conversion formula,

Freq = 108.587 * sqrt( 0.6 / Eigenvalue )

(http://archive.ambermd.org/201307/0678.html)

But, the first frequency gave a very small eigenvalue (in the range of e-06)

Am I proceeding in the right direction?

I need your valuable suggestions in calculating the percentage variance of

each eigenvector.

Thanks in advance..

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Sun Jan 25 2015 - 08:00:03 PST

Custom Search