VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Feb 23 2009 - 14:46:18 CST

On Mon, 23 Feb 2009, Shuo Li wrote:

SL> Dear Sir or Madam:

dear shuo li,

SL> I have run Atom-centered Density Matrix Propagation (ADMP) using the
SL> Gaussian program to produce a dynamic trajectory of a ¡°H+(H2O)21¡±
SL> cluster. Now I hope to use the ¡°IR Spectral Density Calculator
SL> Plugin¡± in VMD to calculate the IR spectra of the ¡°protonated
SL> water cluster¡±. The trajectory file generated by Gaussian can

nice to see that somebody besides me is using it. ;-)

SL> provide dipole-moment-vector data of the whole cluster at each time
SL> step. I can pick up the dipole moment vectors and create a .xyz
SL> file. But I don¡¯t know the specific format of the .xyz file that is
SL> used to calculate the IR spectrum. Can you show me an example? Is it
SL> like the following format?

you don't need an xyz file to generate the spectrum. just
the dipole moment vectors as a list. please see example 1,
in the documentation of the specden command.

http://www.ks.uiuc.edu/Research/vmd/plugins/irspecgui/

in case you still want to make your life needlessly complicated,
you can RTFM the format of .xyz files on the same server.

http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html

cheers,
   axel.

SL>
SL> 64
SL> 21water.LOG
SL> 2.09346783D-02 -4.99817291D-01 -7.77101857D-01 0
SL> -1.10327861D-02 -4.78698024D-01 -8.12734692D-01 1
SL> -4.26516067D-02 -4.63292760D-01 -8.46110146D-01 2
SL> -7.67777649D-02 -4.38795831D-01 -8.62540921D-01 3
SL> ¡­.
SL>
SL> Thank you very much!
SL>
SL> Shuo Li
SL> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.