From: Josh Vermaas (
Date: Tue Jan 22 2013 - 18:18:52 CST

I believe dynamic bonds will connect ANY atoms in a selection that are
within the distance cutoff of one another. Assuming that "type C H"
selects all carbons and all hydrogens, it should draw all possible
connections between C and H atoms that are within the cutoff distance
apart. If you set the cutoff to something quite high and no bonds are
being drawn, quite likely the selection you have made is empty (ie. VMD
doesn't know of anything that has atomtype C or H).

As to the last questions, it is possible, but you'd have to think
carefully about how you are setting up the atomselections. C-C bonds
happen to be longer than C-H bonds, so in principle very carefully
chosen cutoffs will catch C-C bonds but not C-H bonds. However during
simulation it would be a very strange system where both C-C and C-H
bonds are being made-broken simultaneously, so I'm not sure that dynamic
bonds would be the best way of showing what you are trying to show.

-Josh Vermaas

On 01/22/2013 04:44 PM, Peitong Duan wrote:
> Hello,
> How would I set dynamic bond representations for different groups of atoms? For instance, when I am setting the C-H bond length and I enter "type C H" in "Selected Atoms", no bonds will show up. Also will a selection "type C H" apply to C-C and H-H bond lengths as well? Is it possible to set C-C bonds with a different cut-off than C-H bonds?
> Thanks.