CHARMm Principles

      How to Use This Book

CHARMm Principles describes fundamental operations, concepts, and principles of the CHARMm^® program. The book is designed to provide an introduction to the use of CHARMm. Many of the most frequently used applications of CHARMm are covered. The material in this book applies to CHARMm used as stand-alone software or in conjunction with QUANTA^® or Insight II^®.

The book is divided into the following chapters:

Part One Basic Activities

• Chapter 1, Introduction to CHARMm -- This chapter provides an overview of CHARMm activities and basic information on operations, including commands and command files, input and output operations, file formats, command stream control, CHARMm measurement units, and CHARMm array dimensions.

• Chapter 2, Preparing Models for Energy Calculations -- This chapter describes the information that must be available for each molecular model that you want to study with CHARMm and the sources for that information. Information is included on residue topology files, parameter files, and generating and using coordinates.

• Chapter 3, Performing Energy and Force Calculations -- This chapter describes the CHARMm energy function and energy minimization algorithms that can be used to refine structures or locate stationary points for conformational searching for dynamics simulations.

• Chapter 4, Performing Molecular Dynamics -- This chapter explains how to set up, run, and monitor dynamics simulations. It also describes the use of time sets and correlation functions in dynamics simulations.

• Chapter 5, Setting Constraints and Periodic Boundaries-- This chapter describes the options for tailoring files and data to focus on the parts of a molecular system in which you are interested. These options include setting constraints on atoms, angles, dihedral angles, and other properties, and introducing periodic boundary conditions in energy calculations.

• Chapter 6, Performing Free Energy Simulations -- This chapter describes three methods available in CHARMm for performing free energy simulations. It includes the calculations that are performed using each method, the process of running a simulation, post-processing of data, applying scaling, and using umbrella sampling.

• Chapter 7, Setting Stochastic Boundaries -- This chapter describes basic features and the general procedure for setting up stochastic boundaries.

When you are using this book, also have a CHARMm Dictionary available. Use it to find information on specific commands and keywords used in the example scripts.

Who should use this book

This book is written as though CHARMm is being used as stand-alone software. However, the information, is also applicable to users of CHARMm from within QUANTA or Insight II. All QUANTA or Insight II users should have a version of CHARMm packaged with the QUANTA or Insight II software.

Before you begin

Before you begin to use CHARMm, you should already be familiar with:

• The windowing software on your workstation

• Use of the mouse on the workstation

• Basic UNIX^® commands

• An installed, licensed copy of CHARMm

• A home directory in which subdirectories can be created

Using this book with QUANTA and Insight II books

• This book contains information that supplements the QUANTA and Insight II documentation sets. In particular, this book can be used in conjunction with:

• CHARMm Dictionary Parts I and II

• QUANTA user's guides, including:

QUANTA Basic Operations

QUANTA Generating and Displaying Molecules

QUANTA Simulation, Search, and Analysis

• Insight II manual

• All of which are available online at http://www.msi.com/doc.

• Words in italic represent variables. For example:

runmodeler <input filename>

In this example, the name of the input file that you want to use replaces the value input filename.

• Sample syntax and the examples illustrating the contents of files are presented in a typewriter font. For example, the following illustrates a line in an input file:

ACAM_HAMMH.CRD

• Terms introduced for the first time and words you type are presented in boldface type. For example:

Enter none if there are no restart minima to add.

"The published results were generated using the program CHARMm®. This program is distributed by Molecular Simulations Incorporated."

CHARMm Principles