Step 1 - Set up Atom Types

We’ll be setting up our silica system using atomic (ionic) species, rather than creating an explicitly bound network. So, we need two atomic species for this simulation - an oxygen, and a silicon. First, however, we’ll create some suitable atom types by hand - this is instead of applying a built-in forcefield or loading one in from elsewhere.

Select the   Forcefield   tab

In the Atom Types group, click the Add button located at the top-right

Select silicon in the periodic table dialog

Atom types created in this way are named after the symbol of the relevant element.

This creates an empty atom type in the table, and which we’ll now set some useful interaction parameters.

Change the “Charge” of the new atom type to 2

Change the “SR Form” to LJ to request a Lennard-Jones short-range potential for the atom type

In the “SR Parameters” box enter epsilon=0.175 sigma=1.03

We’ll now use the same process to create an oxygen atom type:

Click the Add button again, and choose oxygen from the periodic table

Change the “Charge” of the oxygen atom type to -1

Change the “SR Form” to LJ

Set the “SR Parameters” to epsilon=0.165 sigma=3.5

You might ask where these values for the short-range interaction parameters come from, and why the charges don’t reflect what you might expect to be “formal” oxidation state charges for the ions. Well, those are both good questions, and the real answer is that there are going to be a variety of combinations of Lennard-Jones epsilon, sigma, and atomic charges that give reasonable structures for silica, and those listed here are good enough for a starting point for us. There are no doubt other forcefields in the literature which suggest different parameters for an atomic/ionic representation of the system - you are free to try those if you wish!

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