From Bioinformatics.Org Wiki
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. It is one of the most user-friendly programs available for this purpose. It is particularly useful for visualizing trajectories, either in Charmm (.DCD) or in PDB (MODEL ... ENDMDL) formats.
- NAMD - NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.