From: Axel Kohlmeyer (
Date: Wed Apr 16 2014 - 00:40:16 CDT

On Apr 16, 2014 1:35 AM, "Mingchao Wang" <> wrote:
> Hi all,
> I am simulating amorphous silicon, and want to calculate the bond angle
distribution in VMD. The first step I want to do is to output all the
formed dynamic bonds. I am wondering is that possible to output these
dynamics bonds in VMD, any command can realize this function?

You could use the topotools plugin to do the low level work for you,
provided you assign suitable covalent radii and are content with a simple
distance cutoff to determine what you would consider a bond.

> Kind regards,
> MC