  Pore forming toxins (PFTs) are virulent proteins released by several species,
including many strains of bacteria, to attack and kill host cells. In this
article, we focus on the utility of molecular dynamics (MD) simulations and the
molecular insights gleaned from these techniques on the pore forming pathways
of PFTs. In addition to all-atom simulations which are widely used, coarse
grained MARTINI models and structure based models have also been used to study
PFTs. Here, the emphasis is on methods and techniques involved while setting
up, monitoring, and evaluating properties from MD simulations of PFTs in a
membrane environment. We draw from several case studies to illustrate how MD
simulations have provided molecular insights into protein-protein and
protein-lipid interactions, lipid dynamics, conformational transitions and
structures of both the oligomeric intermediates and assembled pore structures.
