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Home > Documentation

Navigate to
  • Documentation
  • Tutorials
  • Installation
  • Keywords
  • Introduction
    • General remarks
      • About this Document
      • Summary of Functionality
      • Applicability
      • The utility pdb2adf
    • Concepts and Terminology
      • LINK bonds
      • The ADF QM/MM Hybrid Potential
      • Nomenclature and Terminology
        • Full QM/MM system vs. QM model system
        • Link bonds and capping atoms
        • QM, MM and LI atom types
        • Atom types
        • QM/MM type or QM/MM atom type (MM, QM or LI)
        • Force Field atom type
        • ADF atoms or ADF fragments
      • Partitioning into QM and MM regions
    • Implementation
      • ADF QM/MM
      • Limitations, Bugs and Deficiencies
    • GUI-support
  • ADF QM/MM
    • Input: The Essentials
      • Overview
        • Example Input
      • Defining the Coordinates
      • QMMM key block
      • Restarts
      • Geometry Constraints and Fixing Coordinates of MM atoms
      • Miscellaneous Notes
    • QMMM keyblock options
      • Introduction
      • Example Input
      • Description of Options
    • The Force Field File
      • General Notes
        • Format
        • Force Field Atom types
        • Wild Cards
        • Dummy Atoms
        • Miscellaneous Notes
      • Section by Section Description
    • 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 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.
    • Examples in $ADFHOME/examples/adf
      • QMMM_Butane: Basic QMMM Illustration
      • QMMM_CYT
      • QMMM_Surface: Ziegler-Natta catalysis
  • pdb2adf: transform PDB file to QM/MM input file
    • Overview
      • General description
      • Things to notice
      • Official PDB format
      • Contents of fragment file
      • Contents of solvent box files
    • Usage of pdb2adf
      • Short description
      • An example on protein structure
        • Usage of pdb2adf
        • Contents of the 1DYZ.pdb2adf file generated by pdb2adf
      • An example on solvent shell run
        • Contents of the hoh.pdb file
        • Usage of pdb2adf
        • Contents of the hoh.pdb2adf file generated by pdb2adf
    • Example in $ADFHOME/examples/adf
      • pdb2adf: transforms a PDB file in a QM/MM adf-input file
  • Required Citations
    • QM/MM: Quantum mechanical and Molecular Mechanics model
    • External programs and Libraries
  • References
    • List of Publications Using ADF QM/MM
  • Keywords
QMMM
  • Documentation/
  • QMMM/
  • ADF QM/MM Manual

ADF QM/MM Manual¶

  • Introduction
    • General remarks
    • Concepts and Terminology
    • Implementation
    • GUI-support
  • ADF QM/MM
    • Input: The Essentials
    • QMMM keyblock options
    • The Force Field File
    • Setting up a QM/MM Simulation: a ‘Walk Thru’
    • Examples in $ADFHOME/examples/adf
  • pdb2adf: transform PDB file to QM/MM input file
    • Overview
    • Usage of pdb2adf
    • Example in $ADFHOME/examples/adf
  • Required Citations
    • QM/MM: Quantum mechanical and Molecular Mechanics model
    • External programs and Libraries
  • References
    • List of Publications Using ADF QM/MM
  • Keywords
  • (PDF) ADF QM/MM Manual
Next
AMS Modules
Electronic Structure
ADF: molecular DFT Periodic DFT DFTB & MOPAC
Interatomic Potentials
ReaxFF ML Potentials Force Fields
Kinetics
kMC and Microkinetics Bumblebee: OLEDs
Macroscale
COSMO-RS
Application Areas
Research Topics
Batteries Biotechnology Bonding Analysis Catalysis Heavy Elements Inorganic Chemistry Materials Science Nanoscience Oil & Gas OLEDs Perovskites Polymers Semiconductors Spectroscopy
Where to use AMS?
Industry Government Lab National Supercomputer Academic Research Teaching
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