AMBER Archive (2004)

Subject: Re: AMBER: separate the longitudinal and transverse vibrations frequencies

From: David A. Case (case_at_scripps.edu)
Date: Tue May 04 2004 - 13:15:38 CDT

On Tue, May 04, 2004, xiaowei li wrote:

> However, I am facing a new question how to separate the
> longitudinal and transverse vibrations frequencies and eigenvectors
> because the outputs from AMBER mix all the frequencies and eigenvectors
> together. I want to know if there is any way by which I can get the
> eigenfrequencies and eigenvectors of each direction (x, y, z)
> respectively.

I am not sure that I understand the question. The x,y,z components of the
eigenvectors are available in the "vecs" file, and you can analyze them in
whatever way you wish. A piece of DNA will not have any rigorous separation
between "longitudinal" and "transverse" modes. Modes can be classified
according to the molecular point group of the minimum energy structure, but
this is generally not very useful for macromolecules.

...dac 

-- 

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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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