ADF QM/MM - Contents

• 1 INTRODUCTION
  • 1.1 GENERAL REMARKS
    • About this Document
    • Summary of Functionality
    • Applicability
  • 1.2 CONCEPTS AND TERMINOLOGY
    • LINK bonds
    • The ADF QM/MM Hybrid Potential
    • Nomenclature and Terminology
    • Partitioning into QM and MM regions
  • 1.3 IMPLEMENTATION
    • ADF QM/MM
    • Limitations, Bugs and Deficiencies
• 2 ADF QM/MM
  • 2.1 INPUT: THE ESSENTIALS
    • Overview
      • Example Input
    • Defining the Coordinates
    • QMMM key block
    • Restarts
    • Geometry Constraints and Fixing Coordinates of MM atoms
    • Miscellaneous Notes
  • 2.2 QMMM KEYBLOCK OPTIONS
    • Introduction
    • Example Input
    • Description of Options
  • 2.3 THE FORCE FIELD FILE
    • General Notes
      • Format
      • Force Field Atom types
      • Wild Cards
      • Dummy Atoms
      • Miscellaneous Notes
    • Section by Section Description
  • 2.4 SETTING UP A QM/MM SIMULATION - A `WALK THRU'
    • Example A: Cytocine
      • Step 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 p-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.
• REFERENCES