VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 20 2005 - 17:30:30 CDT

Kurt,
  VMD guesses the atoms' VDW radii based on the atom string
names if they weren't included in the file(s) you loaded
the structure from. Depending on what the atoms are that
you're simulating, the radii vary from 1.0 to 1.9. You can
set the atom radius for atoms with a given name with a
sequence of command like these:
  set sel [atomselect top "name H"]
  $sel set radius 1.0
  $sel delete

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 20, 2005 at 06:18:45PM -0400, Kurt Smith wrote:
> I'm using VMD to visualize MD simulations
> done in LJ units. My question is, how can
> I properly control atom sizes? For instance
> using VDW spheres, if I place one atom
> at (0,0,0) and another at (1,0,0) I cannot
> get the 2 spheres to exactly touch by
> setting the sphere scale to 0.5, to 1, or to
> any other value. Do I need to modify something?
> Thanks
>
> Kurt 

-- 
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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