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General
Introduction
Release 2016
Set up
Mouse
Running Remotely
ADFjobs Queues
MOPAC
SCM menu
Background processes with no interface
scmd: communication between GUI modules
scmjobd: monitor running jobs
Viewing your molecule
Molecule style: Balls and Sticks, Sticks, or Wireframe
Camera position: view direction
3D
Fly to selection
Reset View
Mouse Interaction
Rotate, Translate and Zoom
Selecting
Input
Input: shortcuts and buttons
Keyboard shortcuts
Searching
The ”...” details buttons
Using the “i” info buttons
Searching
Panel search details
Key search details
Documentation search details
Molecule search details
Crystals and Slabs
Periodicity
Building crystals
Build slabs
Crystal menu
Map Atoms To Unit Cell
Map Atoms To Cell
Set Cell Center
Remove Molecules Outside Cell
Builder (packmol)
Building molecules
Bonding mode
Atom Details: Connectors (valency) and Lone Pairs, Atom mass
Pre-optimization
Geometry adjustments
Sliders
Edit box
Move an atom (possibly perpendicular to the screen)
Rotate or translate the selection
Coordinates
Z-Matrix
Set Center Of Mass
Set Origin
Symmetry
Rotate 90
Align
Mirror
Update coordinates via ADFmovie
Bonds
Importing your molecule
Copy/Paste between GUI modules, XYZ coordinates or SMILES
Regions
Proteins (from PDB or mol2 files)
Presets and Defaults
Color Code
Make your own presets
Input options remarks
Empty fields
Spin and Occupation
User Input
ADFjobs
Jobs
Job list: per folder or global
Job status (including WARNING and ERROR info)
Selecting Jobs
Running a job: .run and .job
Job files
Local files
Remote files
Clean Up
Archive jobs
Import / Export jobs
Find job files
Test Job
Queues
Interactive Queue
Sequential Queue
Setting up your own Queues
Dynamic queues
Example Queue configurations for SGE and PBS
Tools: set up many jobs and collect data from many jobs
Prepare: set up many jobs at once
Report: collect data from many jobs
Series of jobs depending on each other
ADFview
Visualization methods
Spinor: spin magnetization density
Fields
Steric Interaction
Properties
Comparing data from several molecules
Temporary Files
Calculating Fields
KFbrowser
Non-expert mode
Expert mode
Conformers
Fukui Function
Minimum Energy Crossing Point
ADFcrs: COSMO-RS
Menu Commands
File menu
Compounds menu
Method menu
Properties menu
Analysis menu
Graph menu
Help Menu
GUI Environment Variables
Required Citations
General References
External programs and Libraries
GUI
Documentation
/
GUI
/
GUI Manual
GUI Manual
ΒΆ
General
Introduction
Release 2016
Set up
Mouse
Running Remotely
ADFjobs Queues
MOPAC
SCM menu
Background processes with no interface
scmd: communication between GUI modules
scmjobd: monitor running jobs
Viewing your molecule
Molecule style: Balls and Sticks, Sticks, or Wireframe
Camera position: view direction
3D
Fly to selection
Reset View
Mouse Interaction
Rotate, Translate and Zoom
Selecting
Input
Input: shortcuts and buttons
Searching
Crystals and Slabs
Builder (packmol)
Building molecules
Importing your molecule
Regions
Proteins (from PDB or mol2 files)
Presets and Defaults
ADFjobs
Jobs
Queues
Tools: set up many jobs and collect data from many jobs
Series of jobs depending on each other
ADFview
Visualization methods
Fields
Properties
Comparing data from several molecules
Temporary Files
Calculating Fields
KFbrowser
Non-expert mode
Expert mode
Conformers
Fukui Function
Minimum Energy Crossing Point
ADFcrs: COSMO-RS
Menu Commands
GUI Environment Variables
Required Citations
General References
External programs and Libraries
(PDF)
GUI
Manual