 also setup a single topology simulation.
<h5>Setup</h5>
In the single-topology simulation it is important to know which atoms on the first ligand should be perturbed into which atoms on the second. If the ligands differ in the number of atoms, as is typical, some atoms need to be perturbed into dummy atoms. Therefore, it is necessary that the larger ligand is perturbed into the small one. In our case, this means that we will perturb ligand 3 into ligand 1. If we look at the structures of the ligands, we se