Contents ADF QM/MM
Table of Contents
1 Introduction
.. 1.1 General remarks
.. 1.2 Concepts and Terminology
.. 1.3 Implementation
2 ADF QM/MM
.. 2.1 Input: The Essentials
.. 2.2 QMMM keyblock options
.. 2.3 The Force Field File
.. 2.4 Setting up a QM/MM Simulation: a 'Walk Thru'
3 pdb2adf: transform PDB file to QM/MM input file
.. 3.1 Overview
.. 3.2 Usage of pdb2adf
References
.. Appendix A. List of Publications Using ADF QM/MM
Keywords
Keywords
-- page with Keywords
CHARGES
ELSTAT_COUPLING_MODEL
FORCE_FIELD_FILE
LINK_BONDS
MASSES
MDC_LEVEL
MM_CONNECTION_TABLE
NEWQMMM
OPTIMIZE
OPTIMIZE: fix_mm_geometry
OPTIMIZE: global
OPTIMIZE: grid
OPTIMIZE: max_gradient
OPTIMIZE: max_steps
OPTIMIZE: md_search
OPTIMIZE: method
OPTIMIZE: mm_notconverged
OPTIMIZE: print_cycles
OUTPUT_LEVEL
WARNING_LEVEL
1.2 Concepts and Terminology
LINK bonds
The ADF QM/MM Hybrid Potential
Nomenclature and Terminology
Full QM/MM system vs. QM model system
Link bonds and capping atoms
QM, MM and LI atom types
Atom types
QM/MM type or QM/MM atom type (MM, QM or LI)
Force Field atom type
ADF atoms or ADF fragments
Partitioning into QM and MM regions
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