AMBER Archive (2006)

Subject: Re: AMBER: Cosine content calculation

From: matteo filandri (fgmlo_at_hotmail.com)
Date: Thu Mar 09 2006 - 04:01:20 CST

Excuse me but in the paper cited, and in the Hess formula (Hess B, Physical
Review E vol 62, n°6,pp8438), lambda is not the wavelenght but the
eigenvalue (nm^2).
In a few words, I need the eigenvalue expressed as in the NO mass-weighted
matrix (nm^2)

thanks

>From: "David A. Case" <case_at_scripps.edu>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: Cosine content calculation
>Date: Wed, 8 Mar 2006 12:09:54 -0800
>
>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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