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Elastic network models (ENMs) have been shown to generate the dominant functional equilibrium motions of biomolecules quickly and efficiently. MAVEN simplifies ENM generation, allows for diverse models to be used, and facilitates useful analyses.
SunlightLB is an open-source 3d lattice Boltzmann code which can be used to solve a variety of hydrodynamics problems, including passive scalar transport problems.
Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.
Moved to GitHub in 2013. This SourceForge project is no longer updated.
Source code and documentation:
stokes: https://github.com/kichiki/stokes
libstokes: https://github.com/kichiki/libstokes
libiter: https://github.com/kichiki/libiter
twobody: https://github.com/kichiki/twobody
RYUON User's Manual: https://github.com/kichiki/RYUON-manual
RYUON : many-particle simulation suite
STOCHSIM is a stochastic simulator for biochemical reactions. The particles are represented as individual software objects which react according to probabilities derived from concentrations and rate constants. Simple spatial structures can be built.