From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 05 2012 - 11:39:49 CDT

Hi,
  I'm happy to answer your further questions below:

On Thu, Jul 05, 2012 at 10:35:17AM -0400, Vikas Varshney wrote:
> John,
> I contacted our computer support people and they have few more minor
> questions. I will appreciate if you could clarify some points. I am copy
> pasting their email as they are not on the VMD forum and couldn't email
> directly
>
> Does the VMD software provide stereo support or are you relying on the
> NVida Quadro to do the stereo?

This question is poorly phrased. The answer is "yes" and "yes", because
BOTH the application and the GPU driver have to support stereo in order
for it to work correctly. VMD can support various stereoscopic displays
without help from the GPU driver, but these are for special displays that
can handle side-by-side or checkerboard stereo modes, and they usually only
work for full-screen displays, not for windowed display modes.

> Ie. Can I run the software on a standard GeForce code and produce side by
> side output?

Yes, but you will not be able to display it on any of the mainstream 3D
monitors, and it has other disadvantages I list below:

> Many of the newer 3D displays are providing support for left/right,
> top/bottom and interlacing modes, so if the application can get the images
> out the display can reorder the pixels.

I don't know of any standard LCD panels that support side-by-side, only a
few HDTV type displays do as far as I know. The other problem with
side-by-side is that it only works if you run the graphics full-screen.
That sort of side-by-side will not work at all for windowed OpenGL display.
The other problem with side-by-side stereo is that you lose half of the
horizontal image resolution, and it makes GUI windows illegible. It works
fine for full-screen graphics-only display, but its useless if you want to
display other non-OpenGL windows on the same display.

VMD isn't like a full-screen video game, it's more like a CAD program.
This is really why the Quadro cards are a much better choice. They fully
support windowed stereo OpenGL rendering....

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

> Thank you kindly,
>
> Best Regards,
> Vikas
> On Tue, Jul 3, 2012 at 1:33 PM, Vikas Varshney <vv0210_at_gmail.com> wrote:
>
> Dear John,
> Thanks for the clear explaination. I will look into it in detail now.
>
> Best Regards,
> Vikas
>
> On Tue, Jul 3, 2012 at 1:01 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> To setup 3-D stereoscopic display on Linux, you'll need to have
> an NVIDIA Quadro card and a set of glasses/emitters and a display
> that they are compatible with. Over the years, our lab has used
> Quadro 4000, 5600, 5800, 6000, and QuadroPlex GPUs to drive our
> various stereo workstations and projectors. Lately we are using
> polarized passive stereo projection systems, and on desktops
> we're using Acer stereo LCD displays with built-in emitters with
> the NVIDIA shutter glasses. Of all of the different options, the
> most important choice (and usually most expensive part) is what
> GPUs you use. If you really plan to do a lot of stereoscopic
> display work, you will want to spend the money to get one of the
> higher-end Quadro cards. Some of the low-end Quadro cards aren't
> really meant for stereoscopic display and don't have enough horsepower
> to do it well. Keep in mind that stereoscopic display requires twice
> as much work, so even the high-end Quadro 6000 cards end up running
> noticably slower when running in stereo than when doing monoscopic
> interactive VMD display.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Jul 03, 2012 at 12:37:48PM -0400, Vikas Varshney wrote:
> > Dear John, Users,
> >
> > I intend to visualize my MD trajectories and molecules of
> interest on
> > Linux (Red Hat Enterprise Linux 5.5 (Tikanga)) in 3D.I will
> highly
> > appreciate if you guys could guide me what hardware I need to get
> > (graphics card, monitors, glasses)?
> >
> > Before writing, I tried searching through archive to see if other
> people
> > have asked the same question but only got two hits.
> > Once from 2010 (related to VMD 1.8.7; it was not very clear to
> me) and
> > other recent one which was focused on Windows (which linked to
> UNC website
> > tutorial to set up simple stereo system).
> >
> > Thanks for your guidance.
> >
> > Best Regards,
> > Vikas
> --
> NIH Resource 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/ 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
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078