From: Jeremiah Babcock (
Date: Tue May 06 2014 - 21:58:36 CDT

     I don't have much to add to the experts' opinions already sent, but I
can say that I use a 3 GB GTX 780 and I haven't seen too much of an
improvement from my previous cards, GTX 9800 or AMD 4970 for a single 1080
monitor for the molecular size range you mentioned. Where I do see a
better performance is in rendering. As for comparing NAMD CUDA performance
with 8 cores and the NVIDIA cards, I went from ~0.495 s/step to 0.092
s/step with a 150K system.

Jeremiah B.

On Tue, May 6, 2014 at 4:01 PM, John Stone <> wrote:

> Hi,
> Beyond what has already been said well by others, I would add
> that for many users the main CUDA-accelerated feature they use
> commonly is the QuickSurf surface representation. If you intend to
> want to animate molecular surfaces, that would be a fairly common case
> that benefits greatly from NVIDIA's CUDA. If you render movies in VMD and
> want to use ray tracing, another feature that's coming in the latest
> version
> of VMD is CUDA-accelerated ray tracing. Both the GPU surface display
> and ray tracing features are fairly memory hungry, so you will want a
> GPU that has at least 3GB of memory or more if tese are interesting to
> you. Just as molecular viz. uses a fair amount of memory on the
> host machine, having more memory on the GPU will also make things
> run faster and more smoothly. The nicest thing about the GPU is that
> you can upgrade it at any later time with only a relatively minor
> expenditure, so I would suggest that you get a good base machine
> that you can run for a few years, get an appropriate GPU now, and
> then plan to get a newer GPU later.
> We will be enabling a bunch of new CUDA kernels for trajectory analysis
> and visualization over the next year, and these will benefit from having
> GPUs with a decent amount of on-board memory, and of course a large core
> count. There will be an increasing degree of support for OpenCL going
> forward, but it appears that it will take a while before the loose ends
> with multi-vendor support in OpenCL libraries are sorted out on Linux,
> for example. For the time being we are focusing our development
> efforts on CUDA because it is simpler to deploy on all platforms,
> and it has many features that are only just now getting added to OpenCL.
> If you take these comments along with those made by Axel and Josh, I
> think you've got some reasonable guidance for the next year.
> Cheers,
> John Stone
> On Tue, May 06, 2014 at 12:08:40PM -0400, Erik Nordgren wrote:
> > Hi folks,
> >
> > I have what must be a very common question, although I tried
> searching the
> > list archives and somehow didn't come up with anything very recent &
> > relevant, so figured I'd post.
> >
> > Basically, I'm just wondering if folks who are accustomed to
> purchasing
> > new hardware regularly could comment with thoughts on the "optimum"
> choice
> > (in terms of power vs. cost) of a GPU to put in a desktop workstation
> > today, for smooth visualization of VMD structures with, say, 100-200 K
> > atoms.A (I assume that the "sweet spot" for choosing a GPU is a
> moving
> > target, with the ever-improving capabilities of cards, which is why
> posts
> > on this subject from over a year ago are probably not very relevant
> > anymore.)A I should add that I'm not in the market for an entire
> > brand-new workstation, but rather considering just upgrading the GPU
> in
> > the linux box I already have (a Dell Precision T3500, few years old
> > already), which at the moment has an NVIDA Quadro NVS 295.
> >
> > As a related question, is it true that the only GPU manufacturer worth
> > seriously considering for VMD is NVIDIA (due to the CUDA
> optimizations)?
> > Many thanks in advance for any & all suggestions!
> >
> > Erik
> > --
> > C. Erik Nordgren, Ph.D.
> > Department of Chemistry
> > University of Pennsylvania
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Phone: 217-244-3349