Defining the Coordinates

The initial coordinates of the full QM/MM system are defined with the ATOMS and GEOVAR key blocks as in a normal ADF run. All input methods allowed by ADF can be used with the exception of the new MOPAC option introduced in ADF1999. For example the coordinates can be defined in Cartesian coordinates as in the example above, by a Z-matrix or by the mixed Z-CART method. It is important to realize that only the initial coordinates of the full or real system are required as input. There is no need to define the coordinates of the QM model system or of the dummy capping atoms. The partitioning of the system into QM and MM regions, and the parameters required to define the capping atoms are given in another part of the input. The program will automatically generate the QM model system and the position of the capping atoms.

IMPORTANT: There is a strict rule concerning the order of the atoms in the ADF input during a QM/MM simulation. Namely, the QM atoms and the LI atoms must precede any MM atoms in the input. The QM and LI atoms can come in any order as long as they come before any MM atoms. The program will check this and abort if this is violated.

ADF atoms and fragments

The typical ATOMS key block in ADF has the following format:

ATOMS
 {n} atom coordinates {f=fragment}
 ...
END

For the QM atoms, the atom labels and fragments should be defined as in a normal ADF run. The atom labels for the MM atoms are not read by the program. Instead, the MM force field atom types for all atoms are defined in the MM_CONNECTION_TABLE subkey block. Similarly if fragments are defined for the MM atoms, the program also ignores these. This is also true of the LI atoms, since in the calculation of the QM model system, capping atoms replace link atoms. The replacement atom type used for the electronic structure calculation is defined in the LINK_BONDS subkey block.