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

From: matteo filandri <fgmlo.hotmail.com>

Date: Thu, 09 Mar 2006 11:01:20 +0100

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.scripps.edu>
*

*>Reply-To: amber.scripps.edu
*

*>To: amber.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
*

*>
*

*>-----------------------------------------------------------------------
*

*>The AMBER Mail Reflector
*

*>To post, send mail to amber.scripps.edu
*

*>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
*

_________________________________________________________________

Personalizza MSN Messenger con sfondi e fotografie!

http://www.ilovemessenger.msn.it/

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Sun Mar 12 2006 - 06:10:18 PST

Date: Thu, 09 Mar 2006 11:01:20 +0100

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

_________________________________________________________________

Personalizza MSN Messenger con sfondi e fotografie!

http://www.ilovemessenger.msn.it/

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Sun Mar 12 2006 - 06:10:18 PST

Custom Search