AMBER Archive (2006)

Subject: Re: AMBER: Cosine content calculation

From: David A. Case (
Date: Thu Mar 09 2006 - 10:33:53 CST

On Thu, Mar 09, 2006, matteo filandri wrote:

> Excuse me but in the paper cited, and in the Hess formula (Hess B, Physical
> Review E vol 62, n6,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)
> >> I have tried to apply this eq. from Andricioaei I. J.Chem.Physics
> >> 2001,115,6289 :
> >>
> >> omega(i)=SQRT[ kT/lambda(i) ]
> >>

In the Andricioeai/Karplus paper, "lambda" has units of mass*length**2, as you
can see from the equation above. The symbols and units in the other paper may
be different -- I'm not familiar with it.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to