AMBER Archive (2006)

Subject: Re: AMBER: Cosine content calculation

From: David A. Case (case_at_scripps.edu)
Date: Wed Mar 08 2006 - 14:09:54 CST

On Wed, Mar 08, 2006, matteo filandri wrote:

> I want calculate the cosine content of my PCs from a Quasiharmonic
> calculation with ptraj. I know that the eigenvalues are in cm^-1
> (mass-weighted matrix) and I need to transform them in nm^2, to apply the
> Hess equation.
> I have tried to apply this eq. from Andricioaei I. J.Chem.Physics
> 2001,115,6289 :
>
> omega(i)=SQRT[ kT/lambda(i) ]
>
> but without successes.
>

It's hard to know what you did, or what you mean by "without success".

In the paper you cite, lambda has units of mass*length**2, and omega
has units of time**-1. Frequencies reported in cm**-1 units generally
need to be converted to s**-1 to use formulas reported in the literature; to do
this you multiply by the speed of light.

[I'm not sure why you need lambda: the frequencies themselves are the
quantities one needs to compute entropies and other thermodynamic
quantitites. But I probably just don't understand what you are aiming at.]

...hope this helps....dac

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