Table of Contents
QM/MM Methods
Overview
QM/MM Methods (i) QM/MM Methodology
The QM/MM Modelling Approach
Historical Overview (i)
Historical Overview (ii)
Hybrid Computational Schemes
Termination of the QM region
Choice of QM Model
Choice of MM model
Valence Force Fields (i)
Valence forcefields (ii)
Shell Model Force fields
Choice of MM Model
Conventional QM/MM Scheme
Subtractive QM/MM Coupling
QM/MM Non-bonded Interactions
Mechanical Embedding
Electrostatic Embedding
Creation of neutral embedding site (i) Neutral charge groups
Creation of neutral embedding site (i) Neutral charge groups
Creation of neutral embedding site (ii) Polar forcefields
Creation of neutral embedding site (ii) Polar forcefields
Creation of neutral embedding site (iii) Double link atoms
Creation of neutral embedding site (iii) Double link atoms
Boundary adjustments
Boundary Adjustments (i) Selective deletion of 1e integrals
Boundary Adjustments (ii) Deletion of first neutral charge group
Boundary adjustments (iii) Charge shift
Boundary adjustments (iv) Gaussian Blur
Gaussian Blur: QM/MM Ethane
Electrostatic Embedding Summary
Polarised embedding schemes
Solid-state Embedding
Polarised Embedding Schemes Summary
QM Termination Schemes
Positioning of link atoms
QM/MM Implementation
QM/MM Software Approach (i)
QM/MM Software Approach (ii)
QM/MM Software Approach (iii)
QM/MM Methods (ii) ChemShell
ChemShell
ChemShell Architecture - Languages
ChemShell Architecture
ChemShell Basics
Very Simple Tcl (i)
Very Simple Tcl (ii)
Very Simple Tcl (iii)
Very Simple Tcl (iv)
ChemShell Object types
ChemShell Object Representations
Object Caching
Object Input and Output
Energy Gradient Evaluators
Module options, using the :
Loading Objects - Z-matrices
Additional Z-matrix features (i)
Additional Z-matrix features (ii)
Loading Data Object - Coordinates
Periodic Systems (i)
Periodic Systems (ii)
Core modules: DL_POLY
DL_POLY forcefield terms
DL_POLY Interface Automatic atom type assigment
DL_POLY Example
DL_POLY with CHARMM Parameters
DL_POLY with CHARMM Parameters
Core modules: Geometry Optimisers
Newopt: Geometry Optimisation Module
Newopt Example - minimisation
Newopt: Transition state determination
HDLCopt Optimiser
HDLCopt Example
GULP Interface
GULP interface example
Molecular Dynamics Module
Molecular Dynamics - arguments
Molecular Dynamics - arguments
Molecular Dynamics - More methods
Molecular Dynamics - Example
QM Code Interfaces
GAMESS-UK Interface
GAMESS-UK Example - Basis library
Hybrid Module
Hybrid Module
Solid-state Embedding Scheme
GULP - GAMESS-UK coupling
Finite Cluster Models for Periodic Systems
QM/MM Modelling for Zeolites
Solid-state embedding for oxide surfaces
QM/MM Methods (iii) CHARMM/GAMESS-UK
CHARMM + GAMESS-UK
Running CHARMM/GAMESS-UK
Adding link atoms
Adding Link atoms: using PATCH
GAMESS-UK input
Environment Variables
Link atom position
Gaussian Blur
CHARMM/GAMESS-UK Developments
Using GAMESS-UK within CHARMM
Enzyme QM/MM Applications
QM/MM Treatment of TIM
QM/MM Treatment of TIM
QM/MM Applications
Practical Session
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