Cain performs stochastic and deterministic simulations of chemical reactions. It can spawn multiple simulation processes to utilize multi-core computers. It stores models, simulation parameters, and simulation results (populations and reaction counts) in an XML format. In addition, SBML models can be imported and exported. The models and simulation parameters can be read from input files or edited within the program. Solvers are implemented as command line executables, which makes it easy to launch batch jobs and simplifies the process of adding new solvers. Solvers include Gillespie's direct method, Gillespie's first reaction method, Gibson and Bruck's next reaction method, Tau-leaping, and Hybrid direct/tau-leaping.
(commercial) CHEMKIN is a powerful set of software tools for solving complex chemical kinetics problems. CHEMKIN allows users to predict the chemical conditions of their system based on variable reactor parameters, inlet gas, and catalyst compositions when applicable. CHEMKIN consists of gas and surface-phase chemical kinetic solvers, and a variety of reactor models that can be used to represent the different systems you are interested in modeling.
Gepasi is a software package for modeling biochemical systems. It simulates the kinetics of systems of biochemical reactions and provides a number of tools to fit models to data, optimize any function of the model, perform metabolic control analysis and linear stability analysis.
Khimera is a software tool for the calculation of thermodynamic and kinetic data of chemical processes based on quantum-chemical data. Khimera is a unique tool that has a user-friendly interface from quantum-chemistry program packages to individual rate constant calculations and further to chemical reactor modeling.