VMD - Visual Molecular Dynamics is described as 'VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting'. There are five alternatives to VMD - Visual Molecular Dynamics for Linux, Mac, Windows and Wine. The best alternative is UCSF Chimera, which is free. Other great apps like VMD - Visual Molecular Dynamics are Jmol (Free, Open Source), Rasmol (Free, Open Source), pymol (Paid) and RasTop (Free, Open Source).
Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. The JmolApplet is a web browser applet that can be integrated into web pages.
RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank.
RasTop is a molecular visualization software adapted from the program RasMol, which was initially developed by Roger Sayle. RasTop is particularly adapted for educational purposes and for the rapid analysis of macromolecules at the bench.