VMD is the tool you need to use when you have to analyze proteins, lipid bilayer assemblies and nucleic acids.

The application allows you to view general molecules, and it even comes with complete support for the Protein Data Bank. It requires you to enter the ID or download the molecule, then it displays the protein structure in a snap.

VMD comes with multiple methods of coloring and rendering a molecule, by using CPK spheres, cartoon drawing, licorice bonds or cylinders.

The tool makes it easier to analyze and animate the trajectory of molecular dynamics. VMD acts as a GUI for an external MD program by animating a molecule simulation.

VMD comes with complete support for GPU accelerated computation and multicore processors. It doesn't have a limit for the number of atoms, residues, molecules and trajectory frames it can use, since these are limited only by the amount of memory you have installed on your Mac.

VMD provides the ability to export graphics to a file which can easily be processed by a large number of ray tracing applications.

VMD includes stereo display capability and provides support for more than 60 different molecular formats.

VMD provides a multiple sequence alignment plugin but it also includes a bioinformatics environment created to organize structure data for nucleic acids and proteins.