VMD (Visual Molecular Dynamics) is a visualization program to visualize, model and analyze biomolecular systems. Can generate PSF (Protein Structure File) files, perform live simulations unsing NAMD and modelize and analize sistems through its plugins. Is also fully compatible with the most part of Molecular file formats(PDB,PSF, CHARM,AMBER...).
The GPU compatibility makes VMD able to manage large atom number biomolecules in various representations.