From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 02 2009 - 10:25:36 CDT

Hi,
  I should add that the Tesla accelerated calculation features
in VMD 1.8.7 are easily accessible if you want to try them out,
both the "coulomb" and "coulombmsm" electrostatics methods available
in the Extensions->Analysis->Volmap Tool plugin are CUDA-accelerated
(by factors of 25x to 44x for upper range Tesla cards),
as well as the implicit ligand sampling tool found in
Extensions->Analysis->Implicit Ligand Sampling (around 20x faster),
and in particular, the new molecular orbital representation (50x to 123x
faster per-GPU for the Tesla cards). Let me know if anyone needs help
testing out the CUDA acceleration on their system.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 01, 2009 at 08:20:22AM -0600, Jacob Story wrote:
>
> Several features in the 1.8.7 release of VMD such as molecular orbital display and electrostatic potential map calculations are accelerated by up to 44x using a NVIDIA GPU using the massively parallel CUDA architecture. These features are discussed in the release notes of VMD 1.8.7, and at http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.7/cuda.html.
>
> With a single NVIDIA Tesla C1060 GPU Computing Processor, performance for the 1.8.7 release of VMD calculations are increased by 20X to 44X compared to using CPU processing alone - and the performance have been shown to scale linearly with multiple Tesla C1060 GPUs.
>
> The NVIDIA Tesla C1060 GPU is a dedicated one teraflop computing add-in device that works as a co-processor to the CPU to handle the computationally intensive portions of VMD analysis and visualization calculations. Built for reliability and long running computations, each Tesla C1060 GPU is powered by 240 parallel computing cores and 4 GB of dedicated compute memory ideal for larger VMD simulations.
>
> For a limited time, VMD users can get a 50% discount on up to four NVIDIA Tesla C1060 GPU Computing Processors.
>
> For further information on the offer and how you can take advantage of the special pricing, please visit: http://www.nvidia.com/object/promotion_nvidia_tesla_gpu.html.
>
> For more information about UIUC's use of GPUs to accelerate VMD and NAMD, please visit: http://www.ks.uiuc.edu/Research/gpu/.
>
> For technical questions regarding VMD acceleration using the GPU, please refer to the VMD mailing list:
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/
>
> This discount offer ends on July 24, 2009.
>
>
> Jacob Story | Inside Tesla Account Manager
> P 877-684-3421| Ext 65322| D 801-622-9679
>
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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