VMD-L Mailing List

From: Nguyen Hoang Phuong (phuong_at_theochem.uni-frankfurt.de)
Date: Tue Sep 30 2003 - 10:12:03 CDT

> Hi,This question might be addressed before but
> could anyone tell me if VMD has a capability to
> vizualize the vibrational, rotational modes
> of each bonds, functional groups in a molecule
> which are calculated by Gaussian?
> Thanks in advance.
> Hitoshi
>
>

Hi,

I don't think VMD can do that job, directly. Why don't you used Molden?

To visualize vibrational modes with VMD, I usually generate a serie of
snapshots in PDB format t_1,t2,...,t_n from the equilibrium structure by
using the algorithm:

x(t_n) = x_eq + eive_i*cos(omega_i*t_n)

where eive_i and omega_i are the eigenvetor and frequency of the mode
which you would like to visualize, respectively.

Then I put all of these snapshot in one file and VMD can read this file
and vizualize a nice movie.

Phuong.