VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 20 2005 - 17:30:30 CDT
- Next message: Luis Rosales: "Re: namd-l: Re: Interactive Simulations, ligand size limits...."
- Previous message: Kurt Smith: "Sphere size"
- In reply to: Kurt Smith: "Sphere size"
- Next in thread: Kurt Smith: "Re: Sphere size"
- Reply: Kurt Smith: "Re: Sphere size"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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 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
- Next message: Luis Rosales: "Re: namd-l: Re: Interactive Simulations, ligand size limits...."
- Previous message: Kurt Smith: "Sphere size"
- In reply to: Kurt Smith: "Sphere size"
- Next in thread: Kurt Smith: "Re: Sphere size"
- Reply: Kurt Smith: "Re: Sphere size"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]