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Hy3S uses advanced MPI parallelized hybrid stochastic simulation methods to quickly compute the dynamics of biochemical networks with thousands of species/reactions. Many features included (see Home Page). An easy-to-use GUI (Matlab req) is included.

Handles Hexahedral, Tetrahedral, Quadrilateral, and Triangle meshes. Lagrangian, Hierarchic, and Monomial finite elements. Interface to PETSc solvers, adaptive mesh refinement, and extreme portablility.

PSI is an open-source program for computing molecular properties using high-accuracy, ab initio, quantum mechanical models.

Spasmos is a Python package that allows scientists to simulate the dynamics of highly collisional plasmas using a number of numerical methods.

ea-fold is a platform to perform protein folding simulations by means of evolutionary algorithms. The program implements a parallelized distributed evolutionary algorithms and a flexible force field.

Very small but powerful object oriented library.

Framework for blockstructured adaptive finite volume methods. Provides MPI-parallelized variant of the Berger-Oliger AMR algorithm for Beowulf-clusters. Uses Clawpack. Visualization and conversion tools for HDF4 files included.