  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 "Molecular Dynamics" we have considered protein
simulations from a dynamical point of view, using Newton's laws. In the current
Chapter, we first take a step back and return to the bare minimum needed to
simulate proteins, and show that proteins may be simulated in a more simple
fashion, using the partition function directly. This means we do not have to
calculate explicit forces, velocities, moments and do not even consider time
explicitly. Instead, we will rely on the fact that for most systems we will
want to simulate, the system is in a dynamic equilibrium; and that we want to
find the most stable states in such systems by determining the relative
stabilities between those states.
