I am trying to make a script to adapt and modify the distances between two monomers I do have. I have build a xyz structure and use Openbabel to construct the Z-matrix of the system. However, I am not sure if there is a simple way of modifying it to adapt the distances of the monomers. For example, for two water molecules, which zmatrix is given by:
0 1 O1 H2 1 r1 H3 1 r2 2 a1 O5 2 r3 4 a2 1 180. H6 5 r4 2 a3 4 d1 H7 5 r4 2 a3 4 -d1 Variables r1 = 1.0 r2 = 1.0 r3 = 1.8 r4 = 1.0 a1 = 104.52 a2 = 90. a3 = 120. d1 = 80.
How would you proceed if you want to keep varying the distances using a small "distance step" to compute properties of the system? For example, between atom 2 and 5.