Table of Contents
ADF-GUI TutorialTable of Contents
Introduction
ADF-GUI modules
ADF installation
UNIX (such as Linux) users
Windows users
Macintosh users
Tutorials
Tutorial 1: ADF-GUI overview: 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
Create the first carbon atom
Create the second carbon atom
Create the oxygen atom
Add the hydrogens
Pre-optimize the geometry
Viewing the molecule
Rotate, translate, or zoom
Atom colors
Revert to default view options
Save picture
Molecular conformation
Rotate such that you look along the C-C axis
Select the top CH3 group
Rotate the selection
Back to Staggered Geometry
Getting and setting geometry parameters
Bond length
Bond angle
Dihedral angle
Coordinates
Extending and changing your molecule
Delete an atom
Change the type of an atom
Change the bond type of an existing bond
Add new (bonded) atoms
Step 3: Select calculation options
Preset
Title
XC functional
Basis set
Integration
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
ADF Output: BOB
Tutorial 2: ADF-GUI overview: excitation energies of ethene
Step 1: Start ADFinput
Step 2: Create your ethene molecule
Step 3: Optimize the geometry
Step 4: Calculate the excitation energies
Select calculations options
Run the calculation
Step 5: Results of your calculation
Logfile: ADFtail
Energy levels: ADFlevels
Excitation spectrum: ADFspectra
Transition density: ADFview
ADF Output: BOB
Closing the ADF-GUI modules
Tutorial 3: ADF-GUI overview: vibrational frequencies 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
Logfile: ADFtail
IR-spectrum (vibrational spectrum): ADFspectra and ADFmovie
Tutorial 4: Structure Building
Step 1: Start ADFinput
Step 2: Building an ethanol molecule
Add a methyl group to the methane
Add the hydroxyl group
Add another 'solvent' ethanol
Step 3: Building a peptide chain
Step 4: Metal complexes and ligands
Predefined Metal Complex Geometries
Bidentate Ligands
Modifying the Plane Angle
Step 5: Your own structures library
Defining your structures
Using dummy atoms
Step 6: Internal Matrix and Linear Transit
Building a biphenyl for a linear transit run
Re-ordering atoms in the internal matrix
Tutorial 5: 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
Tutorial 6: TlH Spin-Orbit Coupling
Step 1. Prepare molecule
Step 2. Set calculation options
Step 3: Run your calculation
Step 4. Results of the calculation
TlH energy diagram
Visualization of spinors
Step 5. Calculate the atomization energy including spin-orbit coupling
The Tl atom
The H atom
TlH atomization energy
Tutorial 7: QM/MM using PDB file
Step 1. Use the visualization options
Step 2. Set up the QM/MM model system
Step 3. Set up the calculation details
Step 4. Save and view the protein in solvent
Step 5. Perform a trivial QM/MM calculation on a small system
Tutorial 8: ADF Fragment Analysis
Step 1. Build Ni(CO)4
Step 2. Define fragments
Step 3. Run the fragment analysis and view the results
Step 4. Build PtCl4H22-
Step 5. Define fragments
Step 6. Run the fragment analysis and view the results
