From: Axel Kohlmeyer (
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.

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


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> Thank you very much!
SL> Shuo Li

Axel Kohlmeyer
   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
If you make something idiot-proof, the universe creates a better idiot.