AMBER Archive (2004)

Subject: Re: AMBER: nmode analysis

From: David A. Case (
Date: Mon May 03 2004 - 12:14:19 CDT

On Mon, May 03, 2004, wrote:

> Thank u for your answer, but i am getting 6 zero eigenvalues, and all of
> my eigenvalues are positive. The problem is after these 6 zero
> eigenvalues, some of the very low frequency modes i am getting some
> strange eigenvectors. The problem is with eigenvectors.( I have 84 atoms,
> and in the eigenvector column, for like 30 cm-1, 40 cm-1 frequencies,
> all values are zero except for 1 atom)

Are you actually looking at the eigenvectors themselves (the "vecs" file) or
at some output from nmanal. (The former is the preferred thing to do.)
Visualizing your normal modes might be a good idea to help sort out what is
actually happening.


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