QMMM key block

The QMMM key block, which is in bold face in example 2.1, is a mandatory key block. This key block is necessary to invoke a combined QM/MM simulation. It contains the connection table and the force field atom types needed to define the molecular mechanics potential. If link bonds are present then it defines the necessary parameters for each link bond.

This section also explains how to specify the Force Field file to use and various other options.

FORCE_FIELD_FILE

Keyword (required, default = amber95.ff)
This keyword simply defines the full path of the force field file to be used for the molecular mechanics potential. The location of the force field file is given after the keyword. The full path can be given, or just the file name. In the latter case, the program looks in the current directory that ADF is executing in.
Examples:

FORCE_FIELD_FILE /home/username/sybyl.ff

FORCE_FIELD_FILE sybyl.ff

MM_CONNECTION_TABLE

Subkey block (required)
This key block defines the connection table, the force field atom types and the partitioning of the full system into QM and MM regions. It is critical that the atoms specified in this key block are in the same order as in the ATOMS key block. This is important, because the program may not detect this type of input error and you would get ridiculous results.

MM_CONNECTION_TABLE
 n FF_LABEL MM_TYPE connection numbers
 ...
END

The labels are defined in the following table.

The connection table should be a fully redundant one. In other words, if atom #1 is bonded to atom #5, they each should have the other atom listed in their connections.
Example:

 1 C_2 QM 2 3 4 5
 2 O_2 QM 1
 3 H QM 1
 4 C_3 QM 1 5 6 7
 5 Cu QM 4 1
 6 H QM 4

A fully non-redundant connection table is also supported. In such a connection table, once a bond is mentioned, it is not mentioned again. In other words, the connection list for any atom cannot contain an atom, which precedes it in the atom numbering.
Example:

 1 C_2 QM 2 3 4 5
 2 O_2 QM
 3 H QM
 4 C_3 QM 5 6 7
 5 Cu QM
 6 H QM

These two connection tables are equivalent. Connection tables that are semi-redundant might cause problems. We recommend the fully redundant connection table.

LINK_BONDS

Required for systems with LINK bonds
This key block required for systems with covalent bonds that cross the QM/MM boundary. These bonds are referred to in this document as the link-bonds. Each link bond has a constant parameter 'alpha' associated with it, which is defined as the ratio of the bond length in the real system and of the capping bond in the model QM system. See Section 1 or reference [1] more details. To determine the alpha parameters for each link bond, one can take the capping atom bond distance in a 'pure QM' calculation of the QM model system and ratio it to the corresponding bond distance in the real system. These ratios are typically around 1.30 to 1.50 when hydrogen as a capping atom. The LINK_BONDS subkey block has the following format:

LINK_BONDS
 atom_a - atom_b alpha replacement_fragment [addremove_force_field_type]
 ....
SUBEND

Example:

LINK_BONDS
 15 - 3 1.42 H H1
 8 - 1 1.40 Cl.dzp Cl
SUBEND

The integers atom_a and atom_b refer to the numbering of the two atoms involved in the link bond. One of the atoms will be a LI type atom whereas the other will be a QM type atom. Atom_a and atom_b must be separated by " - " with at least one space between the integer and the hyphen. In other words '3 - 4' is OK, but not '3- 4' '3 -4'. Atoms need not be in any particular order, and the order of the link bonds is also not important. Following this is the alpha parameter for that specific bond. The replacement_fragment is the ADF atom used for the capping atom in the electronic structure calculation of the QM model system. Often the capping atom is a hydrogen atom, however, it need not be. The replacement_fragment must be present in the FRAGMENT key block in the ADF input file. The addremove_force_field_type need only be present for the AddRemove model [3], and indicates the force field type of the capping atom (similar to FF_LABEL in the MM_CONNECTION_TABLE block).
Important note: It is very important to realize that the Hamiltonian depends on the a parameters used. Thus, when comparing relative energies for example, one has to take care that the a's corresponding to the same bonds are identical.