VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 30 2005 - 10:03:16 CST

Nicolas,
  I've loaded 4 million atoms into VMD before with no problems.
VMD was capable of loading systems of that size even several years ago,
the practical limit is available RAM and your own tolerance for rendering
speed honestly. Be aware that when you work with systems of this size,
you'll need a very fast graphics board if you want to view such large
structures with space filling representations. When working with million-plus
atom structures, I'd suggest becoming familiar with the "points"
representation as that's even easier on the graphics board and host
machine than "lines" is. That being said, it's really no big deal to
load a several million atom structure in VMD, the main question is how
much of the structure you want to see at once. If you want to try a structure
of this size, you can easily use the "solvate" plugin to create a HUGE
water box as a test case for your own experimentation. I've also got some
virus and assembly structures that are in the 500,000 to 2,000,000
atom range if you want to play with something more interesting than just
a huge water box. If you need more help with this, let me know, I can
certainly give you some tips to help keep the demands on your visualization
machine minimized to the degree possible.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 30, 2005 at 09:54:37AM +0200, Nicolas CHARVIN wrote:
> Hi
>
> Is there any existing benchmark concerning the maximum of atoms in a
> molecule VMD is able to load ?
> Within our own MD software, we typically use molecules with approx. 1
> million atoms. So, before writing a plugin to read our files, we'd like to
> know if VMD is able to handle them ?
>
> the only benchmark I found is:
> http://pymol.sourceforge.net/pmimag/compare.html
>
> but, it's limited to 52,000 atoms.
>
>
> Does any of you have loaded a "huge" molecule, on which hardware
> configuration, and with wich results ?
>
> thanks in advance
>
> nicolas
>
>
> --
> Nicolas.Charvin_at_univ-savoie.fr
> LMOPS - Lab. Matériaux Organiques à Propriétés Spécifiques
> Bât IUT - Université de Savoie
> 73376 LE BOURGET DU LAC CEDEX
> Tel: 04-79-75-86-53
>
> http://www.univ-savoie.fr/labos/lmops
> 

-- 
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