VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 07 2002 - 14:27:39 CDT

Hi,
  By default VMD can only animate structures that have multiple coordinate
frames. If you want to use the frequencies to color the structure, you
should be able to color the structure by these frequencies using some
Tcl script that you can write. If you want to draw additional geometry,
or show multiple instances of the atoms or something like that you could
use the "draw" commands. Coloring could be accomplished by writing a Tcl
script that saves your frequency info into the "beta" field of each atom,
similar to the "betacolor_distance" example script in the VMD user's guide:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node182.html

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 07, 2002 at 07:55:30PM +0200, Nguyen Hoang Phuong wrote:
>
> 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
> > 

-- 
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