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

Date: Mon, 26 Jan 2015 11:10:25 +0530

thanks for your reply..

To calculate variance, it is necessary to obtain all the eigen values of a

system. This can be obtained using 'thermo' keyword and 'thermo' runs only

with mass-weighted covariance matrix.

Hence mass-weighted covariance matrix was used.

Is there any other way to calculate variance without using mass-weighted

covariance matrix ?

On Sun, Jan 25, 2015 at 9:53 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

*> Hi,
*

*>
*

*> The actual formula is:
*

*>
*

*> Freq. = TO_CM1 * sqrt( KT / Eigenvalue)
*

*>
*

*> where TO_CM1 is a constant for converting from original eigenvalue
*

*> units to units of frequency (was 108.587 in ptraj but has much higher
*

*> precision in cpptraj) and KT is Boltzmann's constant time temperature
*

*> in Kelvin (originally in ptraj this was hardcoded to 0.6 kcal/mol, but
*

*> in recent versions of cpptraj you can specify the temperature during
*

*> 'diagmatrix'). So according to this, the conversion the other way is:
*

*>
*

*> Eigenvalue = KT / (Freq. / TO_CM1)^2
*

*>
*

*> If I plug your first frequency (0.48444 cm^-1) into this (using
*

*> 108.587 and 0.6 for TO_CM1 and KT respectively) I get ~30145 Ang.^2 *
*

*> amu.
*

*>
*

*> However, is there a reason you chose to mass-weight your covariance
*

*> matrix in the first place? If all you want to do is PCA you should
*

*> just use the coordinate covariance matrix (i.e. 'matrix covar'). I
*

*> think the only real reason you'd want to mass-weight your covariance
*

*> matrix is if you want to perform quasi-harmonic analysis.
*

*>
*

*> Hope this helps,
*

*>
*

*> -Dan
*

*>
*

*> On Sun, Jan 25, 2015 at 8:42 AM, Muthukumaran R <kumaran.bicpu.edu.in>
*

*> wrote:
*

*> > 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
*

*>
*

*>
*

*>
*

*> --
*

*> -------------------------
*

*> Daniel R. Roe, PhD
*

*> Department of Medicinal Chemistry
*

*> University of Utah
*

*> 30 South 2000 East, Room 307
*

*> Salt Lake City, UT 84112-5820
*

*> http://home.chpc.utah.edu/~cheatham/
*

*> (801) 587-9652
*

*> (801) 585-6208 (Fax)
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

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

*>
*

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Received on Sun Jan 25 2015 - 22:00:02 PST

Date: Mon, 26 Jan 2015 11:10:25 +0530

thanks for your reply..

To calculate variance, it is necessary to obtain all the eigen values of a

system. This can be obtained using 'thermo' keyword and 'thermo' runs only

with mass-weighted covariance matrix.

Hence mass-weighted covariance matrix was used.

Is there any other way to calculate variance without using mass-weighted

covariance matrix ?

On Sun, Jan 25, 2015 at 9:53 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

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Received on Sun Jan 25 2015 - 22:00:02 PST

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