  A series of simulations aimed at elucidating the self-assembly dynamics of
spherical virus capsids is described. This little-understood phenomenon is a
fascinating example of the complex processes that occur in the simplest of
organisms. The fact that different viruses adopt similar structural forms is an
indication of a common underlying design, motivating the use of simplified,
low-resolution models in exploring the assembly process. Several versions of a
molecular dynamics approach are described. Polyhedral shells of different sizes
are involved, the assembly pathways are either irreversible or reversible, and
an explicit solvent is optionally included. Model design, simulation
methodology and analysis techniques are discussed. The analysis focuses on the
growth pathways and the nature of the intermediate states, properties that are
hard to access experimentally. Among the key observations are that efficient
growth proceeds by means of a cascade of highly reversible stages, and that
while there are a large variety of possible partial assemblies, only a
relatively small number of strongly bonded configurations are actually
encountered.
