Miscellaneous Notes

Using ADF Dummy Atoms

It is often necessary to use dummy atoms when defining a Z-matrix for a geometry optimization. (Here we are not referring to the capping dummy atoms) Dummy atoms are allowed in a QM/MM simulation and they can be used just as they would in a normal ADF run. There are a few things to remember when using dummy atoms in a QM/MM run.

If a dummy atom is to be used to define the coordinates of QM atoms in a Z-matrix for geometry optimization, the dummy atom must precede any MM atoms in the atom list. In this case one should consider the dummy atom as part of the model QM system.

Atom should be given the Xx force field atom type in the MM_CONNECTION_TABLE key block. (In this way the atom is excluded from the non-bonded pair list)

Do not make any bonds to the dummy atom in the connection table; otherwise the program may require the user to define molecular mechanics potentials involving the dummy atom.

Dummy atoms are allowed in the MM region, however, they will only be used to define the initial coordinates. This is because the MM subsystem is always optimized in Cartesian space where dummy atoms are not necessary.

One can consider dummy atoms as part of the model QM system. For example, the following is not allowed because the dummy atom, which is assigned to the QM region, comes after atoms 5 and 6, which are MM, atoms.

MM_CONNECTION_TABLE
 1 C_2 QM 2 3 4
 2 O_2 QM 1
 3 C_3 LI 1 8 9 10
 4 C_3 QM 1 5 6 12
 5 C_3 MM 4
 6 C_3 MM 4> 
 7 Xx QM 
 8 H MM 3
 ...
SUBEND

The example below is almost identical to the above example except that the dummy atom is assigned as a MM atom. Although this is allowed, this dummy atom will be optimized as a MM atom.

MM_CONNECTION_TABLE
 1 C_2 QM 2 3 4
 2 O_2 QM 1
 3 C_3 LI 1 8 9 10
 4 C_3 QM 1 5 6 12
 5 C_3 MM 4
 6 C_3 MM 4
 7 Xx MM 
 8 H MM 3
 ...
SUBEND

The final example below, is probably what is wanted. Here the dummy atom is a QM atom and comes before any MM atoms. In this way, the dummy atom can be used to define the Z-matrix with the QM model system.

MM_CONNECTION_TABLE
 1 C_2 QM 2 3 4
 2 O_2 QM 1
 3 C_3 LI 1 8 9 10
 4 C_3 QM 1 5 6 12
 5 Xx QM 
 6 C_3 MM 4
 7 C_3 MM 4
 8 H MM 3
 ...
SUBEND

Linear Transit Runs.

The QM/MM option can be used with the LINEAR TRANSIT option in ADF. However, the linear transit parameter or coordinate cannot involve any MM atoms. In other words, the linear transit parameter can only be defined in terms of QM atoms only.

Frequency Runs with QM/MM

At the moment, a FREQUENCY run can not be performed when using a QM/MM potential in ADF. This option has been implemented but has been disabled in this release for further testing.