Structure and Reactivity, Molecular Dynamics

• Single point calculations
• Bond energy calculations
  • Ground state energy
  • Formation energy
  • Atomization energies
  • Chemisorption energies
  • Atomic corrections
  • Open shell systems
  • Impurities
• Geometry optimization
  • Convergence criteria
  • Automatic restarts
  • Lattice optimization
  • Keep all results files
  • Constrained optimization
  • Optimization under pressure / external stress
  • Optimization methods
  • Troubleshooting
• Transition state search
• Linear Transit, PES scan
  • Distance, angle, and dihedral angle coordinates
  • Joint scan coordinates
  • Multidimensional PES scan
  • Lattice scan coordinates for periodic systems
  • Calculate properties for all PES points
  • Troubleshooting
  • Output
• Nudged Elastic Band (NEB)
  • Input
  • Frozen atom constraints
  • Optimizations and convergence criteria
  • Output
  • Troubleshooting
• Intrinsic Reaction Coordinate (IRC)
  • Method details
  • Input
  • Output
• Excited state optimizations
• Molecular dynamics
  • General
  • Constrained molecular dynamics
  • (Re-)Starting a simulation
  • Thermostats and barostats
  • Trajectory sampling and output
  • Lattice deformations (volume regimes)
  • Molecule Gun: adding molecules during simulation
  • Removing molecules during simulation
  • Accelerated dynamics
  • Non-equilibrium MD (NEMD)
  • Applying reflective walls
  • Exit Conditions
• Trajectory replay
• Grand Canonical Monte Carlo (GCMC)
  • General info
  • Method Details
  • Input
  • Output
• Automated PES Exploration
  • Overview
  • Job selection and main options
  • Results: the “Energy Landscape”
  • Continue a PES exploration from a previous calculation
  • Troubleshooting
  • Structure comparison
  • Process Search job
  • Saddle Search job
  • Basin Hopping job
  • Fragmented states
  • Landscape Refinement
  • Creating and/or Extending an Energy Landscape from the Input File
  • Optimizer
  • Binding Sites
  • References