From: Axel Kohlmeyer (
Date: Mon Feb 20 2012 - 06:07:02 CST

On Feb 20, 2012, at 7:01 AM, "winardi, erik" <> wrote:

Hi VMD users,

I am wondering how VMD automatically create the bond in between the atom
for .xyz input file data.
Are VMD using some cut-off distance approximation for it ?

Yes, it tries to guess the element of each atom and assigns a radius based
on that guess and then uses these radii to guess bonds. The bond guess is
not based on radius/distance alone, it also does not place bonds between
pairs of hydrogen atoms.


I open the .xyz, they only have information for the atom type and
coordinate only.

Erik Winardi