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From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Sun, 25 Jan 2015 09:23:35 -0700

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
*

Date: Sun, 25 Jan 2015 09:23:35 -0700

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:

-- ------------------------- 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/amberReceived on Sun Jan 25 2015 - 08:30:05 PST

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