VMD (Visual Molecular Dynamics)
VMD is a molecular graphics program designed for the interactive visualization and analysis of biopolymers such as proteins, nucleic acids, and lipids and membranes. It recognizes many file formats, provides many types of molecule representation, 3D display and photorealistic output. For more information, see VMD home page.
Invoking
To use VMD, first load the vmd module
module add vmd
Then launch the VMD interface
vmd
Getting Help
Help is available at http://www.ks.uiuc.edu/Research/vmd