From: Diez Fernandez, Amanda (
Date: Thu May 11 2017 - 07:35:11 CDT


I need to construct an amorphous silica pore and I am learning how to use the Inorganic Builder Plugin.
To start, I decided to simply build a cube of amorphous silica.
I clicked “Build Device” and used it to build a unit cell of amorphous silica.
Then I clicked “Add Bonds” and added bonds ticking:

  * let VMD generate internal bonds, add bonds that wrap around the periodic boxes
  * Periodic in x, y, z
  * Build angles, dihedrals, include bond count in type

I then saw, for example, that there were oxygen atoms that had been bonded to three other atoms. And that some atoms at the edge of the period box did not have all their bonds. How can I fix this?

Thanks in advance,