AMBER Archive (2004)

Subject: Re: AMBER: nmode analysis

From: sebnem_at_mercury.chem.pitt.edu
Date: Mon May 03 2004 - 11:31:18 CDT

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) The slowest modes
should not have that much localaized motion. I checked my peptide and my
structure is also well minimized. I didn't understand the problem. if u
have any suggestions , i'll really appreciate it.

On Mon, 3 May 2004, David A. Case wrote:

> 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: case_at_scripps.edu
> 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 | http://www.scripps.edu/case
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