ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics
Fig 1
(a) Potentials: Particles are subject to position-dependent external potentials, such as boundary potentials or external fields and interaction potentials involving two, three or four particles. As in MD force fields, bonded potentials are defined within particle groups called “topologies” whose bonding structure is defined by a connectivity graph. (b) Reactions: Most reactions are unimolecular or bimolecular particle reactions. Topology reactions act on the connectivity graphs and particle types and therefore change the particle bonding structure. (c) Simulation box: The simulation box with edge lengths ℓx, ℓy, and ℓz. It can optionally be periodic in a combination of x, y, and z directions, applying the minimum image convention.