Skip to content
Scm logo
Scm logo
  • Amsterdam Modeling Suite
  • Applications
  • Tools
  • Docs & Support
  • Company
    • About us
    • Team
    • Projects & Collaborations
    • Partners & Contributors
    • News
    • Events
    • Careers
    • Pricing & Licensing
    • Contact us
Amsterdam Modeling Suite
Atomistic Scale
Electronic Structure
ADF

Understand and predict chemical properties with our fast and accurate molecular DFT code.

Periodic DFT

BAND & Quantum Espresso: Calculate reactivity, band gaps, optical response, and other properties for periodic systems.

DFTB & MOPAC

Model larger molecules and periodic systems, or prescreen many candidates, with the fast electronic structure methods DFTB and MOPAC.
Interatomic Potentials
ReaxFF

Study large, chemically evolving systems with ReaxFF molecular dynamics.

Machine Learning Potentials

Use preparametrized ML potentials M3GNET, ANI-1ccx or your own models.

Force Fields

GFN-FF, Apple&P, UFF, and more- (polarizable) force fields.
Meso- & Macroscale
kMC and Microkinetics

Predict catalytic turn-over frequencies with microkinetics and kinetic Monte Carlo.
Bumblebee: OLED stacks

3D kinetic Monte Carlo for simulating OLED device-level physics
Fluid Thermodynamics
COSMO-RS

Quick physical property predictions, thermodynamic properties in solution, and solvent screening.

Amsterdam Modeling Suite: computational chemistry with expert support to advance your chemistry & materials R&D

Discover the Suite Pricing & licensing
Tools
Workflows and Utilities
OLED workflows

Automatic workflows to simulate physical vapor deposition and calculate properties for OLED device modeling.
ChemTraYzer2

Automatically extract reaction pathways and reaction rates from reactive MD trajectories.
Conformers

Easily generate, screen, refine, and select conformers. Pass on to other modules for conformational averaging.
Reactions Discovery

Predict chemical (side) reactions from nothing but constituent molecules.
AMS Driver
Properties

Calculate frequencies, phonons, and more. Use forces and energies from AMS or external engines.
PES Exploration

Minimize structures, find transitions states, scan multiple coordinates.
Molecular Dynamics

Use advanced thermo- and barostats, non-equilibrium and accelerated MD, molecule gun.

Monte Carlo

Grand Canonical Monte Carlo to study absorption, (dis)charge processes.
Interfaces
ParAMS

Versatile graphical and python scripting tools to create training sets and parametrize DFTB, ReaxFF, and machine learned potentials.
PLAMS

Versatile python scripting interface to create your own computational chemistry workflows
GUI

Powerful graphical interface to set up, run, and analyze calculations. Even across different platforms.
VASP

Interface to popular plane-wave code VASP. Easily set up PES Scans to create training data.

The SCM team wants to make computational chemistry work for you!

Check out the tutorials Questions? Contact us!
Docs & Support
Downloads
Windows

ams2025.102
Mac

ams2025.102
Linux

ams2025.102

 See all
Documentation
Overview

Documentation links for all our modules and tools

Tutorials

Get started quickly with our Tutorials!
Installation Manual

Quick-start guide and extensive installation manual
Brochures

Brochure and flyers for different applications
Other Resources
Changelog

Latest changes to our binaries
Webinars
Workshops
Knowledgebank

Research highlights
FAQ

General FAQs on licensing.
Pricing and licensing

Price and licensing information.
Consulting & Support
How can we help?
Search
  • Free trial
  • Contact

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¶

QM/MM treats part of the atoms quantum-mechanically (QM) and the other ones by molecular mechanics (MM).

  • (PDF) ADF QM/MM Manual

Table of Contents:

  • 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
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
Tools
Workflows
Conformers OLED workflows Reaction analysis Reaction discovery
AMS Driver
Hybrid Engine Molecular Dynamics Monte Carlo PES Exploration Properties
Python Utilities
ACErxn ParAMS PLAMS pyZacros
Interfaces
GUI VASP Parametrization
Documentation & Support
Downloads Documentation Videos Release notes Changelog Previous releases Webinars Workshops AMS Literature Brochure
Company
About us Careers Contact us Events News Our team Partners & Contributors Projects & Collaborations
Pricing & Licensing
Get a price quote Pricing structure Ordering License terms Resellers FAQ

© SCM – Software Chemistry & Materials 2025 – All Rights Reserved

Privacy Disclaimer Cookies Terms of Use Copyright
Manage Cookie Consent
We use cookies to optimise site functionality and give you the best possible experience.
See our cookie statement for all information.
Functional cookies Always active
The technical storage or access is strictly necessary for the legitimate purpose of enabling the use of a specific service explicitly requested by the subscriber or user, or for the sole purpose of carrying out the transmission of a communication over an electronic communications network.
Preferences
The technical storage or access is necessary for the legitimate purpose of storing preferences that are not requested by the subscriber or user.
Statistics
The technical storage or access that is used exclusively for statistical purposes. The technical storage or access that is used exclusively for anonymous statistical purposes. Without a subpoena, voluntary compliance on the part of your Internet Service Provider, or additional records from a third party, information stored or retrieved for this purpose alone cannot usually be used to identify you.
Marketing
The technical storage or access is required to create user profiles to send advertising, or to track the user on a website or across several websites for similar marketing purposes.
Manage options Manage services Manage {vendor_count} vendors Read more about these purposes
View preferences
{title} {title} {title}