Re: AMBER: nmode analysis

From: David A. Case <>
Date: Mon, 3 May 2004 08:50:44 -0700

On Sun, May 02, 2004, sebnem wrote:

> Hi, I am using nmode analysis module in amber7 to find the normal mode
> frequencies of a small peptide. The frequencies are ok, but some of the
> corresponding eigenvectors of very low frequency modes have all zero
> eigenvectors.

These are probably "translational" modes: the first six eigenvalues (which
should be very close to zero frequency) correspond to rotations and
translations. Generally, it is easy to see from the frequency distribution
that there are six frequencies that are much lower than all the others.

If you are not at a minimum on the potential energy surface, you can also get
imaginary frequency modes (printed as negative) that can be quite localized.
Based on your description, this might also be the case.

....good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Mon May 03 2004 - 17:53:00 PDT
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