Step 2 - Set up a Configuration
Time to create a suitable bulk water configuration for our simulation. We’ll use the predefined “simple random mix” generator to get us going.
Configuration ⇨ Create ⇨ Simple random mix
Choose the water species and press
We now need to set a few parameters in the generator in order to get the correct setup.
Click on the Parameters node to show its options
Check that the value of the "rho" variable is 0.1. This is the default value of density set in all of the predefined configuration generators, and just so happens to correspond to the density (in atoms Å-3) of liquid water at room temperature. The variable will be referenced in the Add node when setting the density of the water species
Click on the Add node to show its options
Make sure that the units for the Density are set to
atoms/A3and that the value is set torho
Increase the Population to 1000
Click to recreate the configuration with our adjusted parameters
Dissolve will ask you at this point if you’re sure you want to discard the current configuration - you can safely say ‘Yes’ here as we haven’t started to run the simulation yet
One thousand water molecules should have a cubic box size of just over 31 Å side length. You will see in the Add node that its Species option is not set to anything, which seems counter-intuitive. Specifying a species here instructs the Add node that $N$ identical copies of the species should be added to the box. In most cases it is preferable to introduce some variety to the geometry of the molecules, and so the Add node can instead reference a CoordinateSets node as the source, and which contains sets of coordinates representing randomised, evolved, or read in (from a file) coordinates for the species.
Before we proceed we’ll tweak the temperature of the configuration.
Set the Temperature to 298 K
Initial, randomised water box containing 1000 molecules