VMD-L Mailing List

From: kr_at_isise.rl.ac.uk
Date: Sat Jun 08 2002 - 02:56:39 CDT

Nguyen Hoang Phuong writes:

> I performed the normal mode analysis by using Gromacs (or
> Charmm). Is it possible to display the vibrations with VMD? or
> Does anyone know how to do that? Thanks in advance.

While I hate to advertise another program, the "viewmol" program can
animate vibrational modes given (a) the structure, (b) frequencies
and (c) mode eigenvectors, and has interfaces to a number of programs.

> thank you very much. I only have the file which contains coordinates of
> the atoms of the minimized structure (which was used to calculate the
> Hessian) and another file contains frequencies.
>
> I would like to see the vibrations of the molecule with different
> frequencies.

It seems like you are lacking the mode eigenvectors (c) in your
analysis. However if you actually have the Hessian you can get these
by diagonalising it.

Sincerely

Keith Refson