Preface

Who should read this book

QUANTA Basic Operations is designed primarily for first-time users, to introduce the basic design, layout, and operating principles of QUANTA^® and to explain procedures for executing basic setup tasks.

What this book contains

This book contains feature and function descriptions that give an overview of QUANTA and its capabilities. Tutorial exercises are combined with descriptions to provide a hands-on introduction to the software. Since the book is designed primarily for new users, neither the descriptions nor the tutorial exercises comprehensively document all aspects of QUANTA.

The book is written assuming that you are familiar with:

Basic UNIX^® commands and file and directory structures.

Windowing software on your QUANTA workstation.

The difference between a shell window and a console window on your QUANTA workstation.

How your workstation mouse works.

Assumptions also are made that you have a home directory where you can create subdirectories and a licensed copy of QUANTA installed on your workstation.

How to use the QUANTA introductory documentation set

This book is part of a documentation set that introduces users to QUANTA. The set consists of:

Basic Operations.

Generating and Displaying Molecules.

Simulation, Search, and Analysis.

Although each book is self-contained, you should be familiar with basic operations to successfully complete building and editing tasks; and you should be familiar with molecule building and editing before proceeding with simulation and analysis.

Within each book, exercises are step-by-step procedures that may be linked across chapters. Datafiles may be modified or reused by several exercises.

Because of the sequential nature of the documentation set and the exercises in each book, you will obtain the most coherent and complete view of the software if you go through the books in the intended order.

Documentation set roadmap

The table below lists key topics and where to find information about them in the introductory set of QUANTA books. Book names are abbreviated:

Ops = Basic Operations.

Gen = Generating and Displaying Molecules.

SSA = Simulation, Search, and Analysis.

Since aspects of a topic may be covered in a number of places, use the indices as an important resource for locating all the information on a topic. If you are reading this as online documentation at Accelrys's website, you can use the search functionality to find information.


For information about	Look at
Understanding program layout and design	Ops Chapter 1
Using operating principles and procedures	Ops Chapter 2
Manipulating molecules and displays	Ops Chapter 2; Gen Chapters 6 and 7
Building structures	Gen Chapters 1, 2, 4, and 5
Editing structures	Gen Chapters 1, 2 and 8; SSA Chapter 4
Applying constraints for CHARMm calculations	SSA Chapter 2
Importing and exporting files	Gen Chapter 8
Executing calculations using CHARMm or external programs	Gen Chapters 2, 3, 4, 6, and 9; SSA Chapter 1
Handling data - visual displays, tables, graphs	Ops Chapter 2; Gen Chapters 6 and 7; SSA Chapters 8 and 9
Performing experimental simulations	Gen Chapter 3, SSA Chapters 1, 3, 4, 5, and 7
Analyzing data	SSA Chapter 6

Conventions

Typographical conventions used in this book include: