From: Shuo Li (liso_at_email.uc.edu)
Date: Mon Feb 23 2009 - 14:05:15 CST

Dear Sir or Madam:
I have run Atom-centered Density Matrix Propagation (ADMP) using the Gaussian program to produce a dynamic trajectory of a ¡°H+(H2O)21¡± cluster. Now I hope to use the ¡°IR Spectral Density Calculator Plugin¡± in VMD to calculate the IR spectra of the ¡°protonated water cluster¡±. The trajectory file generated by Gaussian can provide dipole-moment-vector data of the whole cluster at each time step. I can pick up the dipole moment vectors and create a .xyz file. But I don¡¯t know the specific format of the .xyz file that is used to calculate the IR spectrum. Can you show me an example?
Is it like the following format?
 
64
21water.LOG
2.09346783D-02 -4.99817291D-01 -7.77101857D-01 0
-1.10327861D-02 -4.78698024D-01 -8.12734692D-01 1
-4.26516067D-02 -4.63292760D-01 -8.46110146D-01 2
-7.67777649D-02 -4.38795831D-01 -8.62540921D-01 3
¡­.
 
Thank you very much!

Shuo Li