Software:
molecular dynamics (MD):
Dynamo (http://www.pdynamo.org/mainpages/)
Amber (http://ambermd.org/)
Charmm (http://www.charmm.org/)
Gromacs (http://www.gromacs.org/)
Quantum Mechanics (QM):
Gaussian (http://www.gaussian.com/)
Gamess-UK (http://www.cfs.dl.ac.uk/gamess-uk/index.shtml)
Mopac (http://openmopac.net/)
Rendering and graphics:
VMD (http://www.ks.uiuc.edu/Research/vmd/)
Pymol (http://www.pymol.org/)
Chimera (http://www.pymol.org/)
Docking and ligand binding
Autodock (http://autodock.scripps.edu/)
Dock (http://dock.compbio.ucsf.edu/DOCK_6/index.htm)
