Cerius2 Builders

1       Introduction

Cerius² Builders is a complete guide to the specialized builder modules that can be added to the Cerius² modeling environment to supplement the basic model sketching capabilities provided in the Visualizer.

You need not read this entire documentation set before you start using Cerius². Once you are familiar with the information presented in Cerius² Modeling Environment, you can read only the sections of this documentation set that describe the builder modules that you want to use.

Who should use this documentation

Prerequisites

You should already be familiar with:

• The windowing software on your workstation.

• Use of the mouse on your workstation.

• Basic UNIX^® commands.

• Basic use of the Cerius² interface.

• Quantum mechanical techniques.

Your workstation needs to have:

• Access to a licensed copy of Cerius².

• A home directory in which you can create subdirectories.

• Cerius² Modeling Environment--Basic use of the Cerius² interface and the C²·Visualizer module.

• MSI Forcefield Engines: CDiscover--Use of CDiscover in Cerius², Insight, and standalone modes.

• Cerius² Simulation Tools--The Open Force Field, Force Field Editor, Charges, Minimizer, Dynamics Simulation, Analysis, and Field Calculation modules.

• Cerius² Quantum Mechanics: Quantum Chemistry and Cerius² Quantum Mechanics: Physics--Quantum-mechanics programs in the Cerius² interface.

• Cerius² Command Script Guide--How to capture and replay a script of Cerius² commands and enhance your command scripts with the features of the Tool Command Language (Tcl).

• Cerius² Installation and Administration Guide--Step-by-step instructions for installing and administering Cerius² in your operating environment.

On-screen help is available within the Cerius² environment. It is accessed by clicking the right mouse button while the cursor is over the item in the interface about which you want information. A brief identification of some items appears when you simply allow the cursor to linger over them. Additional help and some demos are accessed from the Help menu.

MSI's website

The URL for the documentattion and customer support areas of MSI's site on the World Wide Web are:

http://www.msi.com/doc/

http://www.msi.com/support/

• Terms introduced for the first time are presented in italic type. For example:

Instructions are given to the software via control panels.

• Keywords in the interface are presented in bold type. In addition, slashes (/) are used to separate a menu item from a submenu item. For example:

Select the View/Colors... menu item means to click the View menu item, drag the cursor down the pulldown menu that appears, and release the mouse button over the Colors... item.

• Words you type or enter are presented in bold type. For example:

Enter 0.001 in the entry box.

• UNIX command dialog and examples of lines in files are represented in a typewriter font. For example, the following illustrates a line in a .grf file:

	CERIUS Grapher File

• Words in italics represent variables. For example:

>		cerius2 -b outputfile scriptfile

In this example, the name of the file to which text output should be directed replaces the value outputfile, and scriptfile is the name of a file containing a command script.