2.4 Setting up a QM/MM Simulation: a 'Walk Thru'
In this section we provide a detailed 'walk thru' of the process of setting up an ADF QM/MM simulation. There will be two examples, the first being a fairly straightforward example and the second one being fairly complex.
Example A: CytocineStep 1. Partitioning the System and the Model QM system
Step 2. Labeling of Atoms (QM, MM or LI)
Step 3. Renumbering of Atoms
Step 4. ADF QM/MM input: Atomic coordinates
Step 5. Connection Table and MM force field types
Step 6. LINK_BONDS
Step 7. Assignment of Atomic Charges
Step 8. Remainder of the QMMM key block
Step 9. Putting it all together: The whole ADF QM/MM input
Example B: Pd+-Ethene pi-complexation Linear Transit
Step 1. Partitioning the System and the Model QM system.
Step 2. Labeling of Atoms
Step 3. Renumbering of Atoms
Step 4. Z-matrix and constraints
Step 5. Connection Table, MM force field atom-types and Force Field Modification
Step 6. LINK_BONDS
Step 7. CHARGES
Step 9. Putting it all together: The whole ADF QM/MM input.
