for part in range(num_atoms//3):
    bondsOH.append((num_Trotter_beads + 1 + 3*part, num_Trotter_beads + 1 + 3*part+1))
    bondsOH.append((num_Trotter_beads + 1 + 3*part, num_Trotter_beads + 1 + 3*part+2))
    bondsHH.append((num_Trotter_beads + 1 + 3*part+1, num_Trotter_beads + 1 + 3*part+2))