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  • Introduction
    • Linear Combination of Energy Terms
    • QM/MM
      • Mechanical embedding
        • Example
        • Supported engines
      • Electrostatic embedding
        • Example
        • Supported engines
    • Capping Atoms
      • Position of the Boundary
      • QM/MM Partitioning Examples
      • Electrostatic Embedding
  • Hybrid Engine Options
    • Sub-engines and EngineIDs
    • Linear Combination of Energy Terms
    • QM/MM
    • Capping
    • Restarts
    • Charges per region
      • Linear Combination of Energy Terms
      • Electrostatic Embedding
  • pdb2adf: transform PDB file to QMMM input file
    • Overview
      • General description
      • Things to notice
      • Official PDB format
      • Contents of fragment file
      • Contents of solvent box files
    • Usage of pdb2adf
      • Short description
      • An example on protein structure
        • Usage of pdb2adf
        • Contents of the 1DYZ.pdb2adf file generated by pdb2adf
      • An example on solvent shell run
        • Contents of the hoh.pdb file
        • Usage of pdb2adf
        • Contents of the hoh.pdb2adf file generated by 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
Hybrid
  • Documentation/
  • Hybrid/
  • Hybrid Engine Manual

Hybrid Engine ManualΒΆ

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
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