Re: AMBER: nmode analysis

From: David A. Case <case.scripps.edu>
Date: Mon, 3 May 2004 10:14:19 -0700

On Mon, May 03, 2004, sebnem.mercury.chem.pitt.edu 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.

....dac

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Received on Mon May 03 2004 - 18:53:01 PDT
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