Hybrid Engine Manual

The hybrid engine affords combining other AMS engines.

Table of Contents:

• Introduction
  • Linear Combination of Energy Terms
  • QM/MM
  • Capping Atoms
• Hybrid Engine Options
  • Sub-engines and EngineIDs
  • Linear Combination of Energy Terms
  • QM/MM
  • Capping
  • Restarts
  • Charges per region
• pdb2adf: transform PDB file to QMMM input file
  • Overview
  • Usage of pdb2adf
• Examples
  • Example: QMMM with various forcefields
  • Example: Mechanical embedding QUILD
  • Example: Hybrid engine with charged regions
  • Example: Loading MM charges for regions
  • Example: Molecular gun with the hybrid engine
  • Example: The effect of specifying atom types, or not
  • Example: The role of specifying the atom types
  • Example: Mixing DFT functionals
  • Example: Using capping atoms in a periodic system
  • Example: Using capping atoms in a periodic system with charges
  • Example: QMMM with capping atoms
  • Example*: Mechanical embedding (QUILD)
  • Example: pdb2adf transforms a PDB file to a QMMM input file
• Keywords
  • Links to manual entries
  • Summary of all keywords
• References