QM/MM Methods

4/7/2003


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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

Author: Paul Sherwood

Email: p.sherwood@dl.ac.uk