  This chapter discusses how the PLUMED plugin for molecular dynamics can be
used to analyze and bias molecular dynamics trajectories. The chapter begins by
introducing the notion of a collective variable and by then explaining how the
free energy can be computed as a function of one or more collective variables.
A number of practical issues mostly around periodic boundary conditions that
arise when these types of calculations are performed using PLUMED are then
discussed. Later parts of the chapter discuss how PLUMED can be used to perform
enhanced sampling simulations that introduce simulation biases or multiple
replicas of the system and Monte Carlo exchanges between these replicas. This
section is then followed by a discussion on how free-energy surfaces and
associated error bars can be extracted from such simulations by using weighted
histogram and block averaging techniques.
