FlightGear Flight Simulator: free open-source multiplatform flight sim
General Mission Analysis Tool
DIS(IEEE 1278.1) Fully Implemented in C++
PySCeS is the Python Simulator of Cellular Systems
A multi-modeling and simulation environment to study complex systems
Prediction of proteinfolding in 2D HP model
Growing suite of proteomics simulations for educational purposes
GMES is a free Python package for FDTD electromagnetic simulations.
Simulation, analysis, and management of the movement of water
realistic truck simulator with 3D graphics done from zero