I don`t know whether there is a plugin to use to calculate such an example. So check for it, it can be easier if there is one.

If you are able to calculate COMs then this is just an algebra problem. You can write a tcl script for that.

1- Find the plane equation since you have 3D coordinates of atoms.

2- Then find the normal vector of this plane

3- Repeat for the other group of atoms.

4- Find the angles between these vectors.

Cheers

There are no electrons in MD simulation, and therefore no pi-pi interactions.

It is often more informative to quantify the interaction between two groups of atoms (such as aromatic rings) in MD simulation energetically (nonbonded interaction energies) rather than geometrically.

As Martin suggested, normal MD simulation means that molecules are treated as point charges. So, all the calculations in MD are based on newtonian equations and not Schrodinger equation where each electron group has different contribution for interaction. So, we cannot calculate the pi-pi interactions using plain MD approach.

You can use QM/MM approach and see if it works and there are any pi-pi interactions involved.

regards

Tanuj

Stacking free energies can be calculated very accurately with classical MD simulations.