VMD-L Mailing List

From: Nguyen Hoang Phuong (phuong_at_theochem.uni-frankfurt.de)
Date: Fri Jun 07 2002 - 12:55:30 CDT

Dear Stone,

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.

Regards,

Phuong
-----

 
> Dear Phuong,
> Is your analysis data stored in a trajectory file of some sort?
> If you can load a trajectory file containing your data into VMD, or
> by loading a sequence of individual structure files with "animate read",
> you can then animate your dynamics etc. Let us know if you need more
> help with this, and if so, tell us more about what files you're working
> with etc.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jun 07, 2002 at 05:13:54PM +0200, Nguyen Hoang Phuong wrote:
> >
> > Dear All,
> >
> > 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.
> >
> > Phuong
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>