VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 10 2011 - 17:29:39 CST

On Mon, Jan 10, 2011 at 4:29 PM, Fahimeh Baftizadeh
<fahimeh.baftizadeh_at_googlemail.com> wrote:

fahimeh,

> thanks John for your reply.
> Let me make my question more clear.
> I have a grid of point which they have intensity as a function of time, they
> are fixed in the space, What I would like to see is
> 1- their intensity change with time (like changing the colors).
> 2- then I would like to apply also the volume slice to have more visual
> information.

what you describe is a visualization problem, that is usually
handled by tools like ParaView (http://paraview.org)
or OpenDX (http://www.opendx.org), and others most of which
are commercial applications. they allow you much more flexible
reading and processing of data compared to VMD.

> I was thinking of generating a file.dx ... but maybe i need a little bit of
> tcl scripting in order to generate a movie, not a single frame.

yes. you can load multiple volumetric data sets and then show
only one of them. here is an old script of mine that does this

http://klein-group.icms.temple.edu/cpmd-vmd/files/au-iso.vmd

with "cube" files (which are grids that also include atoms) you
can use this with .dx files just as well. the multi-molanim GUI
that john mentioned more-or-less does the same thing, but with
whole "molecules" (which in VMD-speak can also refer to a
single graphics visualization without any atoms).

cheers,
    axel.

> Thanks in advance
> Fahimeh
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.