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))