Step 8 - Analysis Sites

Time to calculate some properties, but first we need to create some analysis sites on our ions.

To be consistent with the original study our focal site on the cation will be at the midpoint of the two nitrogens of the imidazolium:

Go to the 1-Ethyl-3-methylimidazolium species tab, Analysis Sites section

Select both nitrogen atoms by holding down the Shift key and clicking on them in the viewer (you can also draw individual boxes around them)

Click Create in the viewer toolbar to create a new site with the origin at the midpoint of the these two atoms

Now select one of the nitrogens on its own and click X Axis in the toolbar to define the direction of the x axis

Finally, select the carbon atom in between the nitrogens and click Y Axis in the toolbar to define the direction of the y axis

Double-click the site in the list and rename it to RingNN

For the anion we’ll use a simple centre-of-mass site:

Go to the Acetate species tab, Analysis Sites section

Select all atoms in the acetate (draw a box around everything with the mouse)

Click Create in the viewer toolbar to create the new site

Enable the Weight by mass option

This locates the site more-or-less on the carbon atom of the carboxylate group

Double-click the site in the list and rename it to COM