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
3.2 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
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