Re: [AMBER] error in nmode calculations

From: Jason Swails <>
Date: Wed, 28 Mar 2012 17:46:54 -0400

On Wed, Mar 28, 2012 at 4:11 PM, Cannon, John F. <> wrote:

> >From your input, you are expecting a nmode calculation using only two
> frames (1 to 10 every 5 frames).
> How could any vibration frequencies be calculated with only two
> conformations?

It's calculated from the Hessian matrix of the system. The vibrational
frequency of each normal mode is just the eigenvalue of that mode

If you're referring to using the mass-weighted covariance matrix
(essentially PCA) to get your modes and frequencies, then you certainly
need more than 2 frames to get any kind of meaningful results. Implemented
in, that's referred to as the quasi-harmonic approximation, which
is distinct from what we're calling normal mode analysis here.

I'm not suggesting that it's good practice to use only 2 conformations for
a normal mode calculation, but it does give you vibrational frequencies,
and it's a good approach for debugging an issue with normal mode

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Wed Mar 28 2012 - 15:30:04 PDT
Custom Search