NWChem High Performance Computational Chemistry Software
- NWChem is a computational chemistry software capable of molecular dynamics simulations. It is designed to run on parallel computers and it is developed by the Pacific Northwest National Laboratory.
- http://www.emsl.pnl.gov/docs/nwchem/nwchem.html

The Fritz Haber Center for Molecular Research
- The primary objectives of the center are to support research in molecular dynamics and encourage cooperation between German and Israeli scientists. The center supports theoretical researches in all branches of chemical physics and biophysics.
- http://www.fh.huji.ac.il/

Gromacs
- A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software.
- http://www.gromacs.org/

The MD Group
- The MD Group is concerned with molecular and mesoscopic dynamics simulation studies of complex biomolecular systems such as biopolymers and lipid aggregates.
- http://md.chem.rug.nl/

Seascape Learning!
- Seascape offers computational chemistry and biology software/services including molecular dynamics calculations.
- http://www.seascapelearning.com

NAMD Scalable Molecular Dynamics
- NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
- http://www.ks.uiuc.edu/Research/namd/

Home page - Dennis Rapaport
- Sections on molecular dynamics include java simulations, visualization and interactivity.
- http://www.ph.biu.ac.il/~rapaport/

Molecular Dynamics
- Focuses on parallel molecular dynamics: algorithms, benchmark timings, codes and simulation results. Includes several article references.
- http://www.cs.sandia.gov/~sjplimp/md.html