VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 28 2007 - 17:17:23 CDT

Hi,
  The new Coulomb map type is _extremely_ computationally
intensive, so we did not yet add it to the menus in the
volmap plugin, as only people that are careful will want
to use it. If you want to do any significant calculations
using the coulomb map type, you'll probably want to use
a test version of VMD that supports the NVIDIA CUDA GPU
acceleration features on their new GPUs (e.g. GeForce 8800 etc)
as they run around 40x faster than the CPU version of the code,
making it far more practical to use. I can provide test versions of
VMD for Linux which support CUDA for thos that want to try
it out and are planning on doing significant calculations.
If you want to run the normal CPU version of the coulomb code
then you'll need to restrict your structure sizes or potential
map resolution to prevent the calculation from taking forever.
We're presently working on another type of coulomb map calculation
method that employs a numerical approximation but should run
much faster particularly in the case of the CPU version.

For the time being, you will need to run the "volmap" text
commands to use the new coulomb map type.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 28, 2007 at 06:03:10PM -0400, Raul Araya wrote:
> Dear VMD users:
>
> I jus installed the VMD 1.86 version for windows and I was trying to use
> the coulomb map from the volmap tool, but it just does not have the option
> of coulomb in the map types. What is happening?
>
> Raúl Araya
> Universidad de Chile 

-- 
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