GUI Manual 2020

This manual contains technical and background information on the Graphical User Interface (GUI).

• (PDF) GUI Manual

Table of Contents:

• General
  • Introduction
  • Release 2020
• Set up
  • Mouse
  • Running Remotely
  • OpenGL3.2+, fallback mode
  • Font issues
  • AMSjobs Queues
  • Quantum ESPRESSO
• 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
• Keyboard Shortcuts
  • AMSinput
  • AMSview
  • AMSmovie
  • AMSlevels
  • AMStail (Logfile)
  • AMSoutput
  • AMSspectra
  • AMSbandstructure
  • AMSdos
  • AMSjobs
• Selecting
• AMSpreferences
  • General
  • Restore defaults
  • Panels
• AMSinput
  • Input: options
  • Input: buttons
  • Searching
  • Crystals and Slabs
  • Builder (packmol)
  • Building molecules
  • Tuning Geometry: translation, rotation, position with respect to plane
  • Importing and exporting your molecule
  • Regions
  • Proteins (from PDB or mol2 files)
  • Presets and Defaults
• AMSjobs
  • Jobs
  • Queues
  • Tools: set up many jobs and collect data from many jobs
  • Series of jobs depending on each other
• AMSview
  • Visualization methods
  • Fields
  • Properties
  • Comparing data from several molecules
  • Temporary Files
  • Calculating Fields
• AMSmovie
  • Geometries
  • Scalar Atomic Properties
  • Atomic Vectors
  • Graphs
  • Temperature Profile
  • Trajectory Analysis
  • Export trajectories to other formats
• KFbrowser
  • Non-expert mode
  • Expert mode
• Conformers
• Fukui Function
• Minimum Energy Crossing Point
• Quantum ESPRESSO
  • Tutorials
  • Input
  • Running
  • Visualization of results
  • Scripting support
• VASP via AMS
  • VASP support in the Amsterdam Modeling Suite
  • Setting up a VASP calculation
  • Running VASP via AMS
  • VASP via AMS without the GUI
• AMStrain
  • General
  • Training set
  • Force field
• AMScrs: COSMO-RS
  • Menu Commands
• Microkinetics (MKMCXX)
• GUI Environment Variables
• Required Citations
  • Authors and General References
  • External programs and Libraries