# Implementation¶

## ADF QM/MM¶

The basic philosophy of the ADF QM/MM implementation has been to treat the MM region as a perturbation to the QM model system. The atoms of the QM model system are controlled by ADF as they would in a regular pure QM run, whereas the MM atoms are treated ‘separately’. For example, when geometry optimization is performed, the Hessian matrix is only generated / updated for the QM model system. This is possible because at each geometry step the MM subsystem is fully optimized (with the QM and LI atoms frozen). One should be aware however that there are not necessarily six zero eigenvalues of the Hessian, as the QM system is coupled to the MM system (and therefore not free to rotate/translate !). When internal coordinates are used to define the structure of the complex, the atoms of the QM model system are optimized using the internal coordinate system, whereas the MM subsystem is fully optimized at each step within the Cartesian coordinate system. Figure 1-6 shows the flow control of the ADF QM/MM implementation.

The geometry optimization of the MM subsystem is controlled separately from the QM system. For example, the default convergence criteria for the MM subsystem are far stricter than that of the QM system. Furthermore, there are options to use global optimization techniques on the MM subsystem, see the detailed description of input options later in this manual.

**Figure 1-6**. Schematic representation of the ADF QM/MM implementation

## Limitations, Bugs and Deficiencies¶

Listed here is a list of known bugs, deficiencies and limitations of the ADF QM/MM implementation. Please contact us if you find new entries to this list.

- The MOPAC input option introduced with ADF99 can not be used with the QM/MM option. The QM/MM feature of ADF requires the traditional ADF input styles. However, all options within the tradition ADF input format can be used, such as CART, ZMAT, and ZCART.
- Geometry constraints cannot be applied to MM atoms when using internal coordinates for optimization. Currently constraints can only applied to MM atoms when the optimization is performed in Cartesian coordinates.
- Linear transit coordinates cannot involve any MM atoms.
- See also the Limitations part at the beginning of this document.