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
AxisAngle module:
| Module | Purpose |
|---|---|
|
AxisAngle |
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 focus on.
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 button at the bottom of the module list on the left
Drag a
Select the new
For the DistanceRange change the Bin Width to
10
For the AngleRange change the Max to
90
Enable the Symmetric option
This will account for the planar symmetry of the benzene ring, and map any calculated angles in the range 90 - 180° back in to 0 - 90°
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 $r$ = 0 in the resulting RDF
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.