Molecular dynamics simulations have become instrumental in replacing
our view of proteins as relatively rigid structures with the
realization that they were dynamic systems, whose internal motions play
a functional role. Over the years, such simulations have become a
central part of biophysics. Applications of molecular dynamics in
biophysics range over many areas. They are used in the structure
determination of macromolecules with x-ray and NMR data, the modelling
of unknown structures from their sequence, the study of enzyme
mechanisms, the estimation of ligand-binding free energies, the
evaluation of the role of conformational change in protein function,
and drug design for targets of known structures. The widespread
application of molecular dynamics and related methodologies suggests
that it would be useful to have available an introductory
self-contained course by which students with a relatively limited
background in chemistry, biology and computer literacy, can learn the
fundamentals of the field. This "Guide to Biomolecular Simulations"
tries to fill this need. The Guide consists of six chapters, which
provide the fundamentals of the field and six chapters, which introduce
the reader to more specialized but important applications of the
methodology.