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

From: David A Case <david.case.rutgers.edu>

Date: Sun, 19 Jul 2020 20:57:58 -0400

On Sun, Jul 19, 2020, German P. Barletta wrote:

*>
*

*>I know from Case's paper on crambin, and this mailing list, that when
*

*>running this kind of analysis with cpptraj (that is, using the matrix
*

*>mwcovar command), eigenvalues are reported in units of cm^-1. Why is that?
*

*>It's supposed to be a diagonalization of a covariance matrix, so the
*

*>eigenvalues should be in units of distance^2 (say, cm^2). Right? Is Amber
*

*>just taking the inverse square and reporting those values? If so, why? Or
*

*>is there something else I'm missing?
*

The key is the "mw" (mass-weighted) part: if you just ask to diagonalize

the covariance matrix, you will get what you describe above. We took

a request to do mass-weighting as an indication that one would most

likely be comparing to either normal mode calculations or experimental

vibrational frequencies.

Note that "wavenumbers" (cm^-1) is a conventional unit, giving

1/wavelength for the fundamental vibrational excitation in the harmonic

limit.: This is proportional to energy, and wavenumbers are often treated

as a unit of energy:

E = h*nu = hc/lambda = hc(1/lambda).

They do *not* correspond to just taking the inverse square-root of a

covariance matrix eigenvalue: mass weighting would make the units all

wrong if you tried to do that.

...hope this helps...dac

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Sun Jul 19 2020 - 18:00:02 PDT

Date: Sun, 19 Jul 2020 20:57:58 -0400

On Sun, Jul 19, 2020, German P. Barletta wrote:

The key is the "mw" (mass-weighted) part: if you just ask to diagonalize

the covariance matrix, you will get what you describe above. We took

a request to do mass-weighting as an indication that one would most

likely be comparing to either normal mode calculations or experimental

vibrational frequencies.

Note that "wavenumbers" (cm^-1) is a conventional unit, giving

1/wavelength for the fundamental vibrational excitation in the harmonic

limit.: This is proportional to energy, and wavenumbers are often treated

as a unit of energy:

E = h*nu = hc/lambda = hc(1/lambda).

They do *not* correspond to just taking the inverse square-root of a

covariance matrix eigenvalue: mass weighting would make the units all

wrong if you tried to do that.

...hope this helps...dac

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Sun Jul 19 2020 - 18:00:02 PDT

Custom Search