# How to create a Z-matrix with two molecules a fixed distance away?

I am trying to determine the intermolecular energies between two molecules (i.e. water and lysine) to find the distance and angular dependence between these interactions.

In the psi4 tutorial, I saw that a Sapt0 energy calculation was used to determine the energies between two benzene molecules, but how would one, for example, find the energies between two benzene molecules at fixed distances and bond angles from each other?

Thank you!

Could you clarify the question?

The topic title is about how to create a Z-matrix, but Z-matrices never occur in your post itself.

Yes, I want to see if there is a simple way to define two molecules some fixed distance away and determine the intermolecular energies of these two molecules as a function of this distance. I have been having trouble finding a way to make a Z-matrix consisting of two molecules at some fixed distance/angle away from one another.

As a result, I have been making these dimer systems in Avogadro, dragging the molecules some distance and orientation away from one another, and am using cartesian coordinates to define the dimer system. However, I wanted to ask if there was a way to construct a Z-matrix or alternative way to set this calculation up.

Please let me know if you would like me to clarify my question more!

I would recommend making a Python script to create the geometries for you. You can write your Python directly in the Psi input file, and Psi will execute it at runtime.

Constructing good Z-matrices for non-covalently bound systems is always a pain, especially when there’s no “obvious” way to choose what interfragment coordinates you should use as your internals, and especially when you need to deal with molecules as large as the ones that I think you’re working with.

If you’re going down the Python route for manipulation, openbabel is quite good for manipulating structures (I’ve used it a fair bit for structure manipulation before performing constrained optimisations). I’ve not tried it for manipulating the relative orientation of two different molecules, though, but it’s probably doable.