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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
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Hybrid
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References
References
ΒΆ
M. Swart, AddRemove: A new link model for use in QM/MM studies.
International Journal of Quantum Chemistry 91, 177 (2003)