Questions about: number of chemical bonds and different force fields

Hi,

I’m using the software Avogadro recently and i have some doubts about the parameter that the software uses for calculations. My attention is focused primarily on the GaN molecule and the two crystalline phases that it presents, hexagonal and cubic. When creating a molecule, the number of chemical bonds to each of Ga atom and N is three (or coordination number three), but is expected four. The possibility of creating a molecule with atoms of Ga and N making four chemical bonds exists, as well as the possibility of performing the calculations of geometry optimization, but when the molecule is saved and open on another occasion in the program this presents again only 3 chemical bonds.

I would like to know if the parameters used in determining the number of chemical bonds can be modified. If there is this possibility, I would like to know how to perform these modifications.

Also, I wonder if there is a possibility of adding other force fields in the software for the calculations in addition to those already in software.

Grateful,

Carlos Guilherme Gonçalves de Azevedo - Graduate student
Graduate Program in Sciences and Technology of Materials
Semiconductors Films Laboratory – Department of Physics
State University of São Paulo – Bauru City – São Paulo - Brazil

On Mon, Apr 29, 2013 at 11:16 AM, Carlos Guilherme Goncalves de
Azevedo cggazevedo@fc.unesp.br wrote:

Hi,

I’m using the software Avogadro recently and i have some doubts about the parameter that the software uses for calculations. My attention is focused primarily on the GaN molecule and the two crystalline phases that it presents, hexagonal and cubic. When creating a molecule, the number of chemical bonds to each of Ga atom and N is three (or coordination number three), but is expected four. The possibility of creating a molecule with atoms of Ga and N making four chemical bonds exists, as well as the possibility of performing the calculations of geometry optimization, but when the molecule is saved and open on another occasion in the program this presents again only 3 chemical bonds.

It would be helpful to know what file format you are using, formats
such as CML and MDL explicitly save the bonds and should preserve
them, whereas XYZ etc have no bonds and Avogadro automatically
performs bond perception when the file is opened.

I would like to know if the parameters used in determining the number of chemical bonds can be modified. If there is this possibility, I would like to know how to perform these modifications.

This is all in Open Babel, and for Avogadro 1.x that is where this
would need to be modified I think.

Also, I wonder if there is a possibility of adding other force fields in the software for the calculations in addition to those already in software.

This is again in Open Babel, and other force fields can be added there
I think. In some of our newer work (Avogadro 2 development) we are
looking at simpler ways to hook in other geometry optimization
tools/libraries so that it is easier to use the best tool for the
chemistry you are interested in.

Hope that helps,

Marcus