  While many good textbooks are available on Protein Structure, Molecular
Simulations, Thermodynamics and Bioinformatics methods in general, there is no
good introductory level book for the field of Structural Bioinformatics. This
book aims to give an introduction into Structural Bioinformatics, which is
where the previous topics meet to explore three dimensional protein structures
through computational analysis. We provide an overview of existing
computational techniques, to validate, simulate, predict and analyse protein
structures. More importantly, it will aim to provide practical knowledge about
how and when to use such techniques. We will consider proteins from three major
vantage points: Protein structure quantification, Protein structure prediction,
and Protein simulation & dynamics.
  In the previous chapter, "Introduction to Protein Folding", we introduced the
concept of free energy and the protein folding landscape. Here, we provide a
deeper, more formal underpinning of free energy in terms of the entropy and
enthalpy; to this end, we will first need to better define the meaning of
equilibrium, entropy and enthalpy. When we understand these concepts, we will
come back for a more quantitative explanation of protein folding and dynamics.
We will discuss the influence of temperature on the free energy landscape, and
the difference between microstates and macrostates.
