VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 03 2014 - 12:35:40 CST

Hi,
  VMD could do this, but you would have to be able produce the
required set of incoming per-frame wavefunction coefficients on-the-fly
from some other source. VMD currently reads the basis set and the arrays
of wavefunction coefficients from a file, e.g. from a GAMESS log file, or a
Molden file. If you were able to produce this data on-the-fly, then VMD
could evaluate the MOs and display them interactively.
One case where this is likely doable is with a tool such as Terachem,
which does the QM calculations on the GPU also.

The density you're asking about it not anything like simple volumetric fog...
Each point in space is is the linear combination of GTOs, requiring the
evaluation of polynomial basis set equations with each term containing
exponential functions. In principle these can be evaluated on-the-fly
during rendering, but it is difficult to do that in a work-efficient
way as part of any conventional rendering process. A more work efficient
scheme is what we do in VMD, where the density values are computed in a
first-step, and then rendering is performed, using the previously computed
density map as input. Once you have the density map computed, you
can use a wide range of isosurface extraction or direct volume rendering
or ray casting methods to make images of it. The hard part is really
the rapid calculation of the density map, and the production of
of the wavefunction arrays that go into it as input.

If you wanted to do something that is greatly simplified, there are
probably many other schemes besides what I've described here. The
method I've described is what we did for VMD, to allow visualization
of the output of real QM tools such as GAMESS, and others. If you're
willing to take shortcuts or numerical appriximations I bet you could
do something much simpler than what we did.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 31, 2014 at 04:05:24PM +0000, Douglas Houston wrote:
> Hi all,
>
> Does anyone know of any software that can do 'real-time' orbital rendering?
>
> What I'm looking for specifically is a way to visualise electron
> density (including how it changes in response to e.g. van der Waals
> influences), for teaching and for structure-based ligand design
> purposes. It would be a way for the user to see e.g. induced
> dipole-dipoles being set up as they move two molecules closer
> together, etc. Appearance-wise, in my mind's eye the density is just
> that; something like a "volumetric fog" effect, which is already
> implemented in OpenGL and DirectX:
>
> A few conceptual examples:
>
> http://images-mediawiki-sites.thefullwiki.org/01/3/9/9/84026051836614279.jpg
> http://www.gorkin.com/VolumeRenderer/volumeRenderer.html
> www.hourences.com/tutorialimages/ue3fog/7.jpg
>
> I guess it would need some way of parsing the output of the
> (GPU-accelerated, presumably) MO calculator into GPU API commands?
>
> Would expecting to be able to see real-time shifts in density as the
> user interactively moved atoms/molecules around be reasonable? Or is
> that still too computationally expensive?
>
> I think there are people already working on something like this idea
> for VMD - what stage is it at?
>
> cheers,
> Doug
>
> _____________________________________________________
> Dr. Douglas R. Houston
> Lecturer
> Institute of Structural and Molecular Biology
> Room 3.23, Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
> http://tinyurl.com/douglasrhouston
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/