Hi,
I am working with two molecules (A and B) and would like to place them at a specified separation distance đť‘Ą, defined as the distance between their centers of mass. What is the correct and standard way to construct such a geometry?
Additionally, if I want to consider a fully three-dimensional setup—where the relative position of molecule B with respect to molecule A is specified using Cartesian coordinates
(𝑥,𝑦,𝑧) or alternatively in polar/spherical coordinates—what is the appropriate procedure to define this arrangement in practice?
Can anyone help me with this?