About this Document

This document did not change since the adf2002.03 version, apart from the pdb2adf documentation, which is available in the official release of adf2005.01.

This document describes the QM/MM option within ADF, how to use it, how to set up inputs, what features are available, what its limitations are, and so on. This manual assumes that the reader already has experience with ADF and has some basic knowledge of molecular mechanics (MM) and combined QM/MM theories. A brief overview of the combined QM/MM methods is included.

This document is organized in the following manner. First, concepts and naming conventions that are used throughout the document are introduced. In Chapter 2, setting up a QM/MM simulation with ADF is discussed with a detailed description of all the input options (sections 2.1 and 2.2) and the Force Field files (section 2.3). Section 2.4 contains a 'walk through' of how to set up QM/MM jobs.

The combined QM/MM code and the documentation are in continuous development. We appreciate any comments, bug reports and suggestions for its improvement.