VMD-L Mailing List

From: Rachel (comeonsos_at_googlemail.com)
Date: Thu Aug 02 2007 - 12:31:33 CDT

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
>
>
>