QuanteMM

Contents

Release 2000, March 2000

Contents

1. Introduction

Introduction

2. Theory

The Potential Energy Surface

The Schrödinger equation

The Born-Oppenheimer approximation

Equation for electronic motion - The potential energy surface

Equation for nuclear motion on the potential energy surface

Empirical Fit of the Surface

Molecular dynamics and mechanics

The Forcefield

Classical forcefields

Quantum and classical descriptions of bonds

Utility of the classical approach

Limitations of the classical approach

The Classical Energy Expression

Example energy expression for water

A more realistic example

The Melding of Quantum Mechanical and Molecular Mechanical Surfaces

Link/Capping Atoms

Coupling Between Quantum and Molecular Mechanics

"Surface" Effects

Example (Zeolites): Shifting of Point Charges

3. Implementation

Changes to MOPAC

Organization of the QuanteMM User Interface

Input Files for the Quantum Mechanical Programs

Input files for the Molecular Mechanics Program Discover_3

The embedder(3.0.0)/qmmm(95.0) Background Job

The Steps of a Hybrid QM/MM Calculation

Summary

Background Job Shell Scripts

4. Command Summary

Setup Pulldown

QM_MM_Info Command

Define_QM_Region Command

QM_MM_Systems Command

QM_MM_Parameters Command

Keywords for the QM Calculation: MOPAC

Parameters for the QM Calculation: DMol

Parameters for the QM Calculation: Turbomole

Viewing the Keyword Settings

Parameters for the MM calculation: Nonbond Energy

Nonbond Energy Summation Method

Forcefield Pulldown

Select Command

Potentials Command

Background_Job Pulldown

Setup_Bkgd_Job Command

Completion_Status Command

Kill_Bkgd_Job Command

Run Pulldown

Run_QM_MM Command

5. Methodology

Example: Si(OH)₄ Molecule Embedded In Quartz, SiO₂(

Example: Si(OH)4 Molecule Embedded In Quartz, SiO2()

DMol and QuanteMM

Basic Steps to prepare the DMol Input for QuanteMM

Step 1: Defining the Molecule

Step 2: Setting up the Calculation Parameters

Step 3: Creating Input Files for the DMol Calculation

Commands in the DMol Module relevant to QuanteMM

Beginning a DMol Session

Defining the Molecule and Its Point-Group Symmetry

The Setup/Parameters command

Turbomole and QuanteMM

Basic Steps to prepare the Turbomole Input for QuanteMM

Step 1: Defining the Molecule

Step 2: Setting up the Calculation Parameters

Step 3: Creating Input Files for the Turbomole Calculation

Commands in the Turbomole Module relevant to QuanteMM

Beginning a Turbomole Session

Defining the Molecule and Its Point-Group Symmetry

Specifying Parameters that Control the Calculation

Using the Setup/Parameters Command

Calculation Methods and Electron Correlation

Choosing which Method To Use

Selecting the Basis Set

Using the Basis Set Library

Using Effective Core Potentials

Reading Basis Sets and ECPs from a User-Supplied File

Controlling Disk and Memory Usage

Defining the Electronic State

Setting up the SCF Portion of a Turbomole Job

Environment Parameters

6. Tutorials

Pilot Online Tutorials

A. References

References to Hybrid QM/MM methodology :

General References (QM):

B. File Formats

Input Files

Output Files

C. Background_Job