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

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

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/

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

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

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/

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/