6. Multiscale Simulations

Multiscale Simulations

• 6.1. Overview on ORCA’s Multiscale Implementation
  • 6.1.1. Combining Multiscale Features with other ORCA Features
  • 6.1.2. Required Settings for a Multiscale Simulation
  • 6.1.3. QM and Active Region Definition
    • 6.1.3.1. Explicit Definition of QM and Active Region
    • 6.1.3.2. Automated Definition of QM and Active Region
      • 6.1.3.2.1. Identifying Important Atoms or Functional Groups
      • 6.1.3.2.2. Including Surrounding Atoms
      • 6.1.3.2.3. Applying Rules to Avoid Artifacts
      • 6.1.3.2.4. Automated procedure in ORCA 6.1
      • 6.1.3.2.5. Steps of the Automated Procedure (Illustrated for QM Region; analogous steps apply for active regions)
    • 6.1.3.3. Definition of QM and Active Region via pdb file
  • 6.1.4. Active Atoms in Combination with Optimization, Frequency Calculation, MD
    • 6.1.4.1. Optimization in redundant internal coordinates
    • 6.1.4.2. Optimization with the Cartesian L-BFGS Minimizer
    • 6.1.4.3. Frequency Calculation
    • 6.1.4.4. Nudged Elastic Band Calculations
    • 6.1.4.5. Molecular Dynamics
  • 6.1.5. Boundary Region
    • 6.1.5.1. Link Atoms
    • 6.1.5.2. Bonded Interactions at the QM-MM Boundary
    • 6.1.5.3. Charge Alteration
  • 6.1.6. Embedding Types
  • 6.1.7. Additional Keywords
• 6.2. Multiscale Simulations of molecular systems
  • 6.2.1. Additive QMMM
    • 6.2.1.1. Basic Usage
  • 6.2.2. ONIOM Methods: General Overview
    • 6.2.2.1. Available QM2 Methods
    • 6.2.2.2. Electrostatic Interaction between high and low level
    • 6.2.2.3. Boundary Region
  • 6.2.3. Subtractive QM/QM2 Method (ONIOM2)
    • 6.2.3.1. System charges and multiplicities
    • 6.2.3.2. Solvation
  • 6.2.4. QM/QM2/MM Method (ONIOM3)
    • 6.2.4.1. QM2 Atoms
    • 6.2.4.2. System charges and multiplicities
    • 6.2.4.3. Basic Usage
• 6.3. CRYSTAL-QMMM
  • 6.3.1. Charge Convergence between QM and MM region
  • 6.3.2. MM-MM Interaction
  • 6.3.3. Preparing CRYSTAL-QMMM Calculations
  • 6.3.4. MOL-CRYSTAL-QMMM
    • 6.3.4.1. Extending the QM Region
    • 6.3.4.2. Basic Usage
  • 6.3.5. IONIC-CRYSTAL-QMMM
    • 6.3.5.1. Boundary Region
    • 6.3.5.2. Extending the QM Region
    • 6.3.5.3. Net Charge of the Entire Supercell
    • 6.3.5.4. Example Input
    • 6.3.5.5. Different QM and MM regions Stored in the PDB file
• 6.4. QM/MM via Interfaces to ORCA
  • 6.4.1. ORCA and Gromacs
  • 6.4.2. ORCA and pDynamo
  • 6.4.3. ORCA and NAMD
• 6.5. Fast Multipole Method
  • 6.5.1. The Octree hierarchy
  • 6.5.2. Approximation of the Far Field interactions
  • 6.5.3. The “Very” Fast Multipole Method (VFMM)
  • 6.5.4. Recommended input
  • 6.5.5. Some examples