[[http://www.ks.uiuc.edu/Research/namd/ | NAMD]] is a parallel molecular dynamics code for large biomolecular systems. 

[[http://www.charmm.org/ | CHARMM]] (Chemistry at HARvard Molecular Mechanics) is a program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations.

[[http://www.gromacs.org/ | GROMACS]] is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

[[http://www.accelrys.com/products/ | Accelrys]] provides simulation and informatics software for researchers working in drug discovery and the development of chemicals and materials

[[http://amber.scripps.edu/ | The Amber]] Molecular Dynamics Package. Amber is a package of programs for molecular dynamics simulations of proteins and nucleic acids

[[http://mackerell.umaryland.edu/MacKerell_Lab.html | MacKerell Laboratory:]] empirical force field parametrization

[[http://swissparam.ch/ | swissparam:]]This service provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS.