VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Thu Aug 02 2007 - 15:16:01 CDT

Hi,

measure contacts doesn't take into account the vdw radii of the atoms.
 If you want to do that, it should be reasonably straightforward and
efficient to first extract the radii of all the atoms into a list, run
measure contacts with a cutoff of, say, 5, and then loop over contact
pairs and compare the distances between the pairs to the average of
the vdw radii of the two atoms.

Cheers,
Justin

On 8/2/07, Rachel <comeonsos_at_googlemail.com> wrote:
> Dear VMD community,
>
> Can anyone tell me when two atoms collide, how much should be the distance
> between them if using measure contacts $distance selection1 selection2? or
> is there any other way to define two atoms collide with each other in VMD?
> Thanks in advance.
>
> Regards,
> Rachel
>
>
>
> On 7/31/07, Rachel <comeonsos_at_googlemail.com> wrote:
> >
> > Dear VMD community,
> >
> > By using measure contacts cutoff selection1 selection2, all atoms in
> selection1 that are within cutoff of any atom in selection2 and not bonded
> to it are listed out. What I want to ask is, does this cutoff distance
> include the vdw radius of atoms in selection2? what I want to do is find the
> atom list of atoms in selection1 that are with contact(collides) with atoms
> in selection2, and I assume they are in contact with each other if the
> distance between them are less than the sum of their vdw radii. So if in
> selection2 are all carbon atoms (with vdw raidus= 1.7Angstrom) and in
> selection1 are all oxygen atoms (vdw=1.52 Angstrom), then in my case should
> I define the cutoff as 1.52 or as 3.2? thank you for your help.
> >
> > Kind regards,
> > Rachel
> >
> >
>
> 

-- 
    I speak of certain afternoons in early fall, waterfalls of
immaterial gold, the transformation of the world, when everything
loses its body, everything is held in suspense,
    and the light thinks, and each one of us feels himself thought by
that reflective light, and for one long moment time dissolves, we are
air once more...
                      -- Octavio Paz, "I speak of the city"