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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

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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.

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Home > Documentation

Navigate to
  • Documentation
  • Tutorials
  • Installation
  • Introduction
    • Starting the GUI: start ADFjobs
      • UNIX (such as Linux) users
      • Windows users
      • Macintosh users
    • GUI modules
    • Keyboard shortcuts
  • GUI overview tutorials
    • Getting started: Geometry optimization of ethanol
      • Step 1: Preparations
        • Start ADFjobs
        • Make a directory for the tutorial
        • Start ADFinput
        • Undo
      • Step 2: Create your molecule
        • Create a molecule
        • Viewing the molecule
        • Molecular conformation
        • Getting and setting geometry parameters
        • Extending and changing your molecule
      • Step 3: Select calculation options
        • Preset
        • Title
        • XC functional
        • Basis set
        • Numerical quality
        • Other input options
      • Step 4: Run your calculation
        • Save your input and create a job script
        • Run your calculation
      • Step 5: Results of your calculation
        • Logfile: ADFtail
        • Files
        • Geometry changes: ADFmovie
        • Orbital energy levels: ADFlevels
        • Electron density, potential and orbitals: ADFview
        • Browsing the Output: ADFoutput
    • Building Molecules
      • Step 1: Start ADFinput
      • Step 2: Search for ethanol
      • Step 3: Import XYZ for ethanol
      • Step 4: Import SMILES string
      • Step 5: Build ethanol using the structure tool
      • Step 6: Building a peptide chain using the structures tool
      • Step 7: Metal complexes and ligands
        • Predefined Metal Complex Geometries
        • Bidentate Ligands
        • Modifying the Plane Angle
      • Step 8: Your own structures library
        • Defining your structures
        • Using dummy atoms
      • Step 9: A sphere of Cu atoms, cut out of the crystal
      • Step 10: A carbon nanotube
    • Building Crystals and Slabs
      • The Crystal Structures Tool
      • The Crystal Structures Database
      • Crystal builder (from space group information)
      • Slicer: building slabs
        • A three layer slab of the Cu(111) surface
      • Enlarging the unit cell
  • ADF-GUI tutorials
    • Spectroscopy
      • Excitation energies and UV/Vis spectrum of ethene
        • Step 1: Start ADFinput
        • Step 2: Create your ethene molecule
        • Step 3: Optimize the geometry
        • Step 4: Calculate the excitation energies
        • Step 5: Results of your calculation
        • Step 6: Excited state geometry optimization and excited state density
      • Vibrational frequencies and IR spectrum of ethane
        • Step 1: Start ADFinput
        • Step 2: Create your ethane molecule
        • Step 3: Optimize the geometry
        • Step 4: Calculate the vibrational frequencies of ethane
        • Step 5: Results of your calculation
    • Analysis
      • Fragment Analysis
        • Step 1: Build Ni(CO)4
        • Step 2: Define fragments
        • Step 3: set up the fragment analysis run
        • Step 4: Run the fragment analysis and view the results
        • Step 5: Build PtCl4 H2 2-
        • Step 6: Define fragments
        • Step 7: Run the fragment analysis and view the results
      • Caffeine Bader (AIM) analysis, Benzene NBO visualization and Occupations
        • Step 1: Setup and optimize Caffeine
        • Step 2: Calculation setup
        • Step 3: Orbitals, Potential and AIM results
        • Step 4: Benzene Bader charge analysis and NBOs
        • Step 5: Occupations
      • Visualization of densities, orbitals potentials, ...
        • Step 1: Get Single-Point calculation results with ADF on Anthracene
        • Step 2: Details: Divergent and Rainbow Colormap, scalar range of field on isosurface
        • Step 3: Multi Isosurface
        • Step 4: Combining visualization techniques
        • Step 5: Play with lights
        • Step 6: Special fields
      • Fukui Functions and the Dual Descriptor
        • Step 1: Setting up the calculation
        • Step 2: The output
        • Step 3: Visualizing the Fukui functions and Dual Descriptor
    • Relativistic Effects
      • TlH (thallium hydride) Spin-Orbit Coupling
        • Step 1: Prepare molecule
        • Step 2: Set calculation options
        • Step 3: Run your calculation
        • Step 4: Results of the calculation
        • Step 5: Calculate the atomization energy including spin-orbit coupling
    • Multiple Jobs, Multi-Level, Multiple Compounds
      • Generating a batch of jobs and collecting results: Basis Set Effects for NH3 Geometry
        • Step 1: Create and pre-optimize your molecule
        • Step 2: Set up a single ADF calculation
        • Step 3: Set up a batch of ADF jobs
        • Step 4: Run your set of ADF jobs
        • Step 5: Analyze results of several calculations at once
      • Multi-Level principles: Regions, QUILD, QMMM, Quality per region
        • Step 1: Regions for multi-level calculations, visualization and grouping
        • Step 2: QUILD
        • Step 3: QMMM
        • Step 4: Quality per region
      • Multiple molecules, conformers, multiple methods
        • Multipe molecules
        • Conformers
        • Multiple Methods
    • Structure and Reactivity
      • Spin Coupling in Fe4S4 Cluster
        • Step 1: Create and pre-optimize the Fe4 S4 cubane model
        • Step 2: Obtain the solution for the high-spin (HS) state of the cubane
        • Step 3: Couple the spins in Fe4 S4 using the SpinFlip option
        • Step 4: Coupling the spins using the ModifyStartPotential option, use ARH SCF convergence method
        • Step 5: View the spin density of the broken symmetry (BS) solutions
      • HCN Isomerization Reaction
        • Step 1: Prepare the HCN molecule
        • Step 2: Create a rough approximation for the transition state geometry
        • Step 3: Finding the transition state: prepare approximate Hessian
        • Step 4: Search for the transition state
        • Step 5: Calculating frequencies at the transition state
        • Step 6: Following the reaction coordinate
        • Step 7: Following orbitals along the IRC: reporting from .t21 files
        • Step 8: Following orbitals for the LT afterwards: generating jobs for many geometries
      • Transition State Search with ASE using the Nudged Elastic Band method
        • Step 1: Build the initial and final molecule
        • Step 2: Set the calculation details
        • Step 3: Viewing the Results
  • BAND-GUI tutorials
    • Bonding Analysis
      • Bandstructure/DOS/Charges/Orbitals/Densities - With a Grain of Salt
        • Step 1: Start ADFinput
        • Step 2: Set up the unit cell
        • Step 3: Add the atoms
        • Step 4: Running the calculation
        • Step 5: Examine the band structure
        • Step 6: Visualizing the results
        • Step 7: Check the charges
      • Periodic Energy Decompositon Analysis - PEDA
        • Step 1: Start ADFinput
        • Step 2: Set up the system - CO@MgO(sqrt(2)xsqrt(2))
        • Step 3: Running the PEDA calculation
        • Step 4: Checking the results
      • PEDA for Spin Unrestricted Calculations
        • Step 1: Start ADFinput
        • Step 2: Set up the system - Ethane
        • Step 3: Running the PEDA calculation
        • Step 4: Checking the results
      • PEDA + NOCV - decomposing the orbital relaxation term
        • Step 1: Setting up the System and the Calculation
        • Step 2: Checking the results
        • Step 3: Plotting NOCV orbitals and deformation densities
      • PEDA-NOCV for Spin Unrestricted Calculations
        • Step 1: Start ADFinput
        • Step 2: Set up the system - Ethane
        • Step 3: Running the PEDA-NOCV calculation
        • Step 4: Checking the results
        • Step 5: Plotting NOCV orbitals and deformation densities
    • Model Hamiltonians
      • NiO and DFT+U
        • Step 1: adfinput
        • Step 2: Setup the system - NiO
        • Step 3: BP86 without Hubbard
        • Step 4: Run the calculation - BP86+U
    • Structure and Reactivity
      • Transition State Search with a Partial Hessian
        • Step 1: Create the system
        • Step 2: Calculate a partial Hessian
        • Step 3: Transition state search with a frozen substrate
  • DFTB-GUI tutorials
    • DFTB charges, frequencies and dynamics (MD)
      • Step 1: DFTB: Pre-optimization and Charges
      • Step 2: Frequency evaluation
      • Step 3: Molecular dynamics
    • Periodic DFTB, Lattice Optimization, DOS, band structure and phonons
      • Step 1: Lattice optimization - input setup
      • Step 2: Lattice optimization - execution
      • Step 3: DOS and Band Structure
      • Step 4: Phonons
    • Proton affinities with third order DFTB (DFTB3)
      • Step 1: Optimization of the neutral molecule
      • Step 2: Optimization of the acetate and the hydrogen ions
    • UV/Vis spectrum of Ir(ppy)3
  • MOPAC-GUI tutorial
    • Toluene charges, movies, frequencies and normal modes
      • Set up Toluene in MOPACinput
      • Run interactively
      • Save job and results: charges and movies
      • IR spectrum and normal modes
  • ReaxFF-GUI tutorials
    • Burning methane
      • Step 1: Start ReaxFFinput
      • Step 2: Create a methane / oxygen mixture
      • Step 3: Prepare for burning: set up the simulation
      • Step 4: Burn it: run the simulation
      • Step 5: Analyze it: Create a reaction network
      • Step 6: Analyze it: Browse a reaction network
      • Step 7: Analyze it: Filter a reaction network
    • Water on an aluminum surface
      • Step 1: Start ReaxFFinput
      • Step 2: Creating the surface
      • Step 3: Add solvent
      • Step 4: Set up the simulation, including a temperature regime
      • Step 5: Run the simulation
  • COSMO-RS GUI Tutorials
    • COSMO result files
      • Step 1: Start ADFinput
      • Step 2: Create the molecule
      • Step 3: ADF COSMO result file
      • Step 4: MOPAC COSMO result file
    • Overview: parameters and analysis
      • Step 1: Start ADFcrs
      • Step 2: Add Compounds
      • Step 3: Set pure compound parameters
      • Step 4: COSMO-RS and COSMO-SAC parameters
      • Step 5: Visualize the COSMO surface: ADFview
      • Step 6: Analysis: The sigma profile
      • Step 7: Analysis: The sigma potential
    • Overview: properties
      • Step 1: Start ADFcrs
      • Step 2: Vapor pressure
      • Step 3: Boiling point
      • Step 4: Flash point
      • Step 5: Activity coefficients, Henry coefficients, Solvation free energies
      • Step 6: Partition coefficients (log P)
      • Step 7: Solubility
        • Solubility liquid in a solvent
        • Solubility solid in a solvent
        • Solubility gas in a solvent
      • Step 8: Binary mixtures VLE/LLE
        • Isothermal
        • Isothermal, input pure compound vapor pressure
        • Isothermal, miscibility gap, LLE
        • Isobaric
      • Step 9: Ternary mixtures VLE/LLE
        • Isothermal
        • Isobaric
      • Step 10: A composition line between solvents s1 and s2
    • The COSMO-RS compound database
      • 4.1: Install and use the COSMO-RS compound database
        • Step 1: Install database
        • Step 2: Add or search compounds
        • Step 3: Set pure compound data
        • References
        • Step 4: Visualize the COSMO surface: ADFview
      • 4.2: Octanol-Water partition coefficients (log POW )
        • References
      • 4.3: Henry’s law constants
        • References
      • 4.4: Solubility of Vanillin in organic solvents
        • References
      • 4.5: Binary mixture of Methanol and Hexane
        • References
      • 4.6: Large infinite dilution activity coefficients in Water
        • References
      • 4.7: Parametrization of ADF COSMO-RS: solvation energies, vapor pressures, partition coefficients
        • Table: Parametrization of COSMO-RS
        • References
      • 4.8: COSMO-SAC 2013-ADF
        • References
    • pKa values
      • 5.1: Empirical pKa calculation method
      • 5.2: Relative pKa calculation method
    • Ionic Liquids
      • 6.1: Install and use the ADF COSMO-RS ionic liquid database
        • References
      • 6.2: Ionic liquid volumes and densities
        • References
      • 6.3: Activity coefficient calculation
        • References
      • 6.4: Henry’s law constants
        • References
      • 6.5: Gas solubility and selectivity in ionic liquids
        • References
      • 6.6: VLE for systems containing ionic liquids
  • Scripting tutorials
    • PLAMS
      • First steps with PLAMS
        • Running the script
        • Molecule
        • Settings class
        • Creating and running the Job
        • Results
      • Automating Workflows
        • Introducing the case study
        • Workflow script
        • Settings library
        • Miscellaneous remarks
Tutorials
  • Documentation/
  • Tutorials/
  • GUI tutorials

GUI tutorials¶

  • Introduction
    • Starting the GUI: start ADFjobs
    • GUI modules
    • Keyboard shortcuts
  • GUI overview tutorials
    • Getting started: Geometry optimization of ethanol
    • Building Molecules
    • Building Crystals and Slabs
  • ADF-GUI tutorials
    • Spectroscopy
    • Analysis
    • Relativistic Effects
    • Multiple Jobs, Multi-Level, Multiple Compounds
    • Structure and Reactivity
  • BAND-GUI tutorials
    • Bonding Analysis
    • Model Hamiltonians
    • Structure and Reactivity
  • DFTB-GUI tutorials
    • DFTB charges, frequencies and dynamics (MD)
    • Periodic DFTB, Lattice Optimization, DOS, band structure and phonons
    • Proton affinities with third order DFTB (DFTB3)
    • UV/Vis spectrum of Ir(ppy)3
  • MOPAC-GUI tutorial
    • Toluene charges, movies, frequencies and normal modes
  • ReaxFF-GUI tutorials
    • Burning methane
    • Water on an aluminum surface
  • COSMO-RS GUI Tutorials
    • COSMO result files
    • Overview: parameters and analysis
    • Overview: properties
    • The COSMO-RS compound database
    • pKa values
    • Ionic Liquids
  • Scripting tutorials
    • PLAMS
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?
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