VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 19 2010 - 22:07:43 CST

Irene,
  Can you try loading the simple example on the tutorial link I gave
below and let me know if it works for you or not? I actually have an
NVS 290 at the lab, and I believe it should work for this if everything
is installed correctly.

Cheers,
  John

On Tue, Jan 19, 2010 at 10:21:33AM -1000, Irene Newhouse wrote:
> This is what VMD says on startup:
>
> Info) Multithreading available, 4 CPUs detected.
> Info) Free system memory: 2658MB (68%)
> Info) No CUDA accelerator devices available.
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this optional X server feature.
> Info) OpenGL renderer: Quadro NVS 290/PCI/SSE2
> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
>
> Thanks!
> Irene
>
> > Date: Tue, 19 Jan 2010 13:50:55 -0600
> > From: johns_at_ks.uiuc.edu
> > To: einew_at_hotmail.com
> > CC: vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: visualizing APBS output
> >
> >
> > Irene,
> > What graphics card and driver version are you using?
> > (what does VMD print to the console when it starts up?)
> > To do visualizations of high resolution electrostatic maps using
> > the "Color by Volume" feature of VMD, you'll need a GPU that
> > has a good amount of video memory, ideally 512MB or more.
> > I have a simple electrostatics visualization mini-tutorial
> > for VMD available here:
> > http://www.ks.uiuc.edu/Research/vmd/minitutorials/colorbypot/
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Jan 19, 2010 at 09:31:08AM -1000, Irene Newhouse wrote:
> > > I've been running APBS locally. When I have the results displayed with
> the
> > > top molecule, I see nothing. Displaying in a new window works. I've
> been
> > > trying to follow
> > >
> http://apbs.wustl.edu/MediaWiki/index.php/How_do_I_visualize_the_electrostatic_potential_around_my_biomolecule%3F#Isocontour_visualization?
> > > to map the potential to the molecular surface, and I can't get it to
> work.
> > > I can see isosurfaces w/out difficulty, as well as field lines, but I
> > > can't display the surface & color by volume. That website dates from
> an
> > > earlier version of VMD. Is there something slightly different in 1.8.7
> > > that I'm not aware of?
> > >
> > > Thanks!
> > >
> > > Irene Newhouse
> > >
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> > --
> > 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
>
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-- 
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