  Computing reaction rates in biomolecular systems is a common goal of
molecular dynamics simulations. The reactions considered often involve
conformational changes in the molecule, either changes in the structure of a
protein or the relative position of two molecules, for example when modeling
the binding of a protein and ligand. Here we will consider the general problem
of computing the rate of transfer from a subset A of the conformational space
Omega to a subset B of Omega. It is assumed that A and B are associated with
minimum energy basins and are long-lived states.
  Rates can be obtained using many different methods. We review some of the
most popular approaches. We organize the different approaches roughly in
chronological order and under four main categories: reactive flux, transition
path sampling, conformation dynamics. The fourth class of methods, to which we
do not give any specific name, in some sense attempts to combine features from
transition path sampling and conformation dynamics. They include
non-equilibrium umbrella sampling (Warmflash et al. [2007], Dickson et al.
[2009b]), and weighted ensemble dynamics (Huber and Kim [1996]).
