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In the early years of molecular dynamics simulations of biomolecules, almost all scientists working in the field received specialized training (as graduate students and/or postdoctoral fellows) that provided a detailed understanding of the power and limitations of the approach. Now that the methodology is becoming more accessible (in terms of ease of application of generally distributed programs and the availability of the required computational resources) and better validated (in terms of published results), many people are beginning to use simulation technology without training in the area. Molecular dynamics simulations are becoming part of the ‘‘tool kit’’ used by everyone, even experimentalists, who wish to obtain an understanding of the structure and function of biomolecules. This volume has an important role to play in the transition of the field from one limited to specialists (although they will continue to be needed to improve the methodology and extend its applicability) to the mainstream of molecular biology. The emphasis on an in-depth description of the computational methodology will make the volume useful as an introduction to the field for many people who are doing simulations for the first time. By providing detailed information on biomolecular systems that is often experimentally inaccessible, computational approaches based on detailed atomic models can help in the current efforts to understand the relationship of the structure of biomolecules to their function. For that reason, they are now considered to be an integrated and essential component of research in modern biology, biochemistry, and biophysics. In recent years the significant increase in computer power along with the implementation of a wide range of theoretical methods into sophisticated simulation programs have greatly expanded the applicability of computational approaches to biological systems. The expansion is such that interesting applications to important and complex biomolecular systems are now often carried out by researchers with no special training in computational methodologies. To successfully apply computational approaches to their systems of interest, these ‘‘nonspecialists’’ must make several important choices about the proper methods and techniques for the particular question that they are trying to address. This book is organized so that nonspecialists as well as more advanced users can benefit. It can serve as both an introductory text to computational biology, making it useful for students, and a reference source for active researchers in the field. Therefore, the chapters, particularly in Part I, are ordered so that the reader can easily follow from one topic to the next and be systematically introduced to the theoretical methods used in computational studies of biomolecular systems. The remainder of the book is designed so that the individual parts as well as their chapters can be read independently. Additional technical details can be found in the references listed in each chapter. Thus the book may also serve as a useful reference for both theoreticians and experimentalists in all areas of biophysics and biochemical research.This volume thus presents a current and comprehensive account of computational methods and their application to biological macromolecules.