Step 2 - Create Configuration
Of course we need a configuration to use as our calculation / analysis target, and which must represent exactly the data file we’re going to read in terms of atom / species ordering, box size etc. The reference system is a 9 mol% isopropanol in water mix, with 3234 molecules - 291 isopropanol followed by 2943 water. The atom coordinates of the xyz species you used in the previous step also reflect the atom ordering within molecules. The periodic box of the reference simulation is cubic with a side length of 48.6080 Å.
So, let’s set up a random mix to mirror all of this:
Configuration ⇨ Create ⇨ Simple random mix
Highlight both the IPA and water species and press
Let’s now adjust the steps of the generator to reflect what we have in the reference data.
First, we will explicitly set the box size:
Click on the Box node to show its options
Change the A, B, and C box lengths to
48.6080
We want to retain this box size when we add the molecules in, so we need to tell the Add nodes to leave the box alone. We’ll set the required populations at the same time:
Click on the Add node for the IPA species show its options
Change the BoxAction to
None
Change the Population to
291
And for the water:
Click on the Add node for water
Change the BoxAction to
None
Change the Population to
2943
With this set-up, the Parameters node is in fact redundant since our density is defined by our imposed box volume and the populations of the species. The CoordinateSets nodes also no longer have any purpose since we will be overwriting the configuration coordinates with our reference data.