QMMM_Butane: Basic QMMM Illustration¶
Sample directory: adf/QMMM_Butane/
This example is a simple illustration of the QM/MM functionality: half of the butane molecule is treated quantum-mechanically, the other half by molecular mechanics.
$ADFBIN/adf << eor Title BUTANE in Z-matrix input
(Omitted in this printout: the usual specifications of fragments, symmetry, integration accuracy, -)
QMMM FORCEFIELD_FILE $ADFRESOURCES/ForceFields/amber95.ff RESTART_FILE mm.restart OUTPUT_LEVEL=2 WARNING_LEVEL=2 ELSTAT_COUPLING_MODEL=0 LINKS 1 - 4 1.38000 H SUBEND MM_CONNECTION_TABLE 1 CT QM 2 3 4 5 2 HC QM 1 3 HC QM 1 4 CT LI 1 9 13 14 5 CT QM 1 6 7 8 6 HC QM 5 7 HC QM 5 8 HC QM 5 9 CT MM 4 10 11 12 10 HC MM 9 11 HC MM 9 12 HC MM 9 13 HC MM 4 14 HC MM 4 SUBEND End Atoms Internal C 0 0 0 0 0 0 H 1 0 0 B1 0 0 H 1 2 0 B2 A1 0 C 1 2 3 B3 A2 D1 C 1 2 3 B4 A3 D2 H 5 1 2 B5 A4 D3 H 5 1 6 B6 A5 D4 H 5 1 6 B7 A6 D5 C 4 1 2 B8 A7 D6 H 9 4 1 B9 A8 D7 H 9 4 10 B10 A9 D8 H 9 4 10 B11 A10 D9 H 4 1 9 B12 A11 D10 H 4 1 9 B13 A12 D11 End GeoVar ....
In the QMMM key block, the MM connection table identifies the atoms as belonging to either the QM (quantum mechanics) part, or the MM (molecular mechanics) part, or to the set of LI (link) atoms, which define the connection between the QM and the MM regions. Order and numbering are one-to-one with the list under the Atoms key.
The Link atom, part of the MM section of the system, is associated with a capping atom, in the QM part of the system. The Links subkey block specifies for each LI atom defined under the MM_Connection_Table subkey block the chemical type of the replacing capping atom (here: H). On the same line we find the ratio of the QM atom LI atom distance to the QM atom capping atom distance (here: 1.38), and the numbers (1 and 4) of the involved QM atom and LI atom.
The other subkeys in the QM key block are simple subkeys. The specify the file with the force field parameters to be used in the MM subsystem, the (restart) file to write MM data to, print and warning levels and a code for the electrostatic coupling model to use. See the rest of the QM/MM manual for a detailed discussion of all options.
The calculation is a simple geometry optimization (the Geometry key is not displayed here, but is contained in the full input). This consists of a repeated two-step process. At the first step, the MM system is kept frozen, the SCF equations are solved for the QM system, where potentials resulting from the MM system are included, and gradients on the QM atoms are computed from the SCF solution. At the second step, the QM system’s geometry is updated and then kept frozen while the MM system’s geometry is optimized (converged) for that particular QM configuration. And so on, until the whole combined system is self-consistently converged.