The second edition of The Art of Molecular Dynamics Simulation is an enlarged and updated version of the first. The principal differences between the two editions are the inclusion of a substantial amount of new material, both as additional chapters and within existing chapters, and a complete revision of all the software used in the case studies to reflect a more modern programming style. This style change is a consequence of the population shift in the research community. At the time the first edition was written older versions of the Fortran language were still in widespread use; despite this fact, C was chosen as the programming language for the book in preference to Fortran, but in a form that would appear familiar to Fortran programmers of the era. Now that C – and related languages – are in widespread use, and Fortran has even evolved to become more like C, the expressive capabilities of C can be employed to the full, resulting in software that is easier to follow. The power of desktop computers has also increased by a large factor since the case studies of the first edition were developed; in recognition of this fact some of the studies consider larger systems, reflecting a shifting view of what is considered a ‘short’ computation. Other minor changes and corrections have been incorporated throughout the text. The exhortation to employ this volume as a cookbook remains unchanged.