Step 9a - Centre-of-Mass RDF
Examining the centre-of-mass RDF between molecules is often useful since it gives a general picture of the arrangement between molecule. A related quantity is the coordination number, i.e. the number of molecules within solvation shells that typically form around molecules in the liquid. Here we’ll set up calculation of the centre-of-mass RDF and the associated coordination number for the first solvation shell. Dissolve provides a predefined layer to calculate both at once, however first we need to define a suitable site - the centre of mass of the water molecule.
Define the Centre-of-Mass Site
If you don’t already have a site COM representing the centre-of-mass of the molecule, perform the following steps:
Open the
Water species tab and go to the section
In the species viewer to the right, click-drag with the left mouse button and draw a box around all three atoms of the water molecule to select them.
Right-click the selcted atoms and click ⇨
In the section, under Definition select the Weight origin by mass option
Double-click on the new site in the list and change its name to
COM
You’ll see the site represented in the species viewer as a 3D crosshair indicating the coordinates of the origin, surrounded by a small cube.
Create an Analysis Layer
We’ll now create one of Dissolve’s predefined layers to give us the processing modules we need:
Layer ⇨ Create ⇨ Analysis ⇨ RDF & Coordination Number
The new layer contains the following modules:
| Module | Purpose |
|---|---|
SiteRDF |
Calculates the radial distribution function between two specified sites |
We’ll need to set up both of these modules to calculate exactly what we need. First,
SiteRDF:
Select the
Click the SiteA option and choose the
COMsite
Select the
COMsite for SiteB as well
Ensure that the ExcludeSameMolecule option is enabled
Since we are calculating the RDF of a site around itself, the ExcludeSameMolecule option prevents consideration of the same site with itself (which would give a distance of zero and result in a large undesirable spike at the beginning of the RDF). The distance range over which to calculate the RDF can be set in the Control settings group, but the defaults (0 - 10 Å with a step size of 0.05 Å) are fine for what we need.
For the coordination number calculation:
Tick the RangeAEnabled option
Set the maximum for RangeA to 3.4 Å
We can specify up to three separate ranges over which to calculate coordination numbers but we will focus on the first coordination shell in this example.