VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 03 2016 - 15:39:24 CDT

Hi,
  You might try contacting the authors of NMWiz at U. Pittburgh to clarify
questions you still have after reading the documentation since nobody else
on VMD-L seems to have the answer to your question. In particular, I
would expect that Ahmet Bakan would likely know the most about the details
of the output of the NMWiz plugin.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Sep 29, 2016 at 11:33:41PM +0000, Guo, Jiasen (MU-Student) wrote:
> Hi, VMD-users
>
> i am currently work with with VMD plugin NMWiz to visualize eigenvectors
> generated from normal mode analysis. But I have a difficult time to
> understand the second parameter of after the keyword "mode", like, in the
> NMWiz manual, an example is as follows
>
> ...
>
> coordinates 172.541 -33.818 72.141 172.591 -29.981 71.748 171.498 -29.271
> ..
> mode 1 5.08 0.010 -0.014 -0.030 0.011 -0.013 -0.029 0.006 -0.012 -0.027
> ...
> mode 2 3.99 -0.003 -0.014 0.007 0.001 -0.016 0.002 0.001 -0.019 0.000 ...
> mode 3 2.82 0.010 0.027 0.000 0.006 0.028 0.003 0.005 0.028 0.004 0.002
> ...
> ..
>
> the manual explain this parameter as the " mode length (square root of
> variance or inverse frequency) " But if it is the inverse frequency,
> shouldn't it be a very small number (10^-12) for a wave number of about
> 100cm-1, which is not the case in the manual, I guess what i interpret is
> not what the manual wants to say. the information i have is the
> eigenvectors with it cooresponding wavenumber. Can anyone help me
> understand what does this parameter means, or how can i convert wavenumber
> to this parameter. Thanks very much!!!
>
> Best Regards
>
> Jiasen Guo 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/