Cerius²·Forcefield Engines

1       Introduction

This documentation set, Cerius2 Forcefield Engines: OFF, is a guide to decks of cards that are often used by most Cerius² users. Included in the documentation is information on two forcefield modules (OFF and MMFF), the Charges module, and the Minimizer and Dynamics Simulation modules.

The Cerius²·Open Force Field module (OFF) is the foundation module required for many molecular mechanics energy calculations performed in Cerius². The Open Force Field module is a necessary basis for the simulations modules documented here, the Force Field Editor module, and many modules described in other Cerius² documents.

Using this guide

You need not read this entire documentation set before you start using Cerius2 simulation tools:

• First-time users should use lessons in Cerius2 Tutorials (published separately by MSI) to get acquainted with Cerius² and the Cerius²·Open Force Field module.

• Everyone should read the Introduction and familiarize themselves with the introductory material and section headings in Preparing the System, Minimization, Dynamics Simulation, and Analyzing Results.

• The extent to which you actually read Preparing the System, Minimization, Dynamics Simulation, and Analyzing Results depends on what tasks you want to perform and how much you need to customize your calculations.

• Reference material is contained in References and File Formats. Information on using the Force Field Editor to modify or create forcefields is contained in The Forcefield Editor.

Prerequisites

You should already be familiar with:

• How to use the Cerius² graphical interface and what various control types are called (see Cerius² Modeling Environment).

• The theory and general methodology for performing forcefield-based calculations (see Forcefield-Based Simulations).

• The windowing software on your workstation.

• Basic UNIX commands.

• Licensed copies of Cerius2 and the appropriate simulation modules.

• A directory in which you have write permission.

Among the products that require the Open Force Field module are:

ASearch: Mechanical Properties

Blends: MFA (Molecular Field Analysis)

Conformers: Minimizer

Descriptor+: Morphology

Diversity: Polymorph

Dynamics: QSAR+

Force Field Editor: Sorption

IR/Raman

• Forcefield-Based Simulations--A general guide to all MSI's simulation engines. It includes information on all forcefields supported by MSI, as well as theory and general methodology for setting up and performing simulation tasks such as minimization and molecular dynamics.

• Cerius² Modeling Environment--The basic how-to guide for using the Cerius² graphical interface, including model building and environment management.

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

• MSI Forcefield Engines: CDiscover--Using the newer version of Discover (written in C language) in Cerius², Insight II, and standalone modes.

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 URLs for the documentation library and customer support areas of MSI's site on the World Wide Web are:

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

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

Typographical conventions

• 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 file samples 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.