Step 4 - Set up Analysis

For our “properties of interest” we’ll calculate both the centre-of-geometry RDF and the out-of-plane angle between molecules as a function of distance. We can get both from the CalculateAxisAngle module:

Module	Purpose
CalculateAxisAngle	Calculates the distance vs. axis angle map between two sites

Since our site (COG) is set up for the Z axis to be pointing out of the plane of the benzene ring, it is the angle formed between these axes on the different molecules that we’ll consider.

Let’s add an empty processing layer to to the simulation, add on our module, and set it up:

Layer ⇨ Create… ⇨ Empty

Double-click the layer tab and rename it to Analysis

Show the module palette for the current layer by clicking the Show Palette button at the top left of the tab

Drag a CalculateAxisAngle module over to the Current Modules list

Select the CalculateAxisAngle module to show its options

Open the Control settings group

Leave the DistanceRange settings as-is - the defaults are fine

For the AngleRange change the Max to 90 and the Bin Width 10 respectively

Now we must tell the module which sites to use for its calculation:

Set both SiteA and SiteB to COG

Set the AxisA and AxisB to ZAxis

Enable the ExcludeSameMolecule to prevent the unwanted self-correlation spike at 0 in the resulting RDF

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It would also be nice here to calculate the spatial density function (the three-dimensional distribution of molecules around a reference point) and compare it, but this takes more iterations than a (sane) example will allow.