VMD

VMD is a molecular visualization program installed on all workstations and clusters. The official documentation can be found here with some tutorials here. Like gnuplot however, the wealth of options means that often it takes a long time to find the one command you need to use so below you will find some useful basic settings/info for using VMD. For producing graphics for publication, Pymol is probably a better option as it has a built in ray-tracing routine but for general visualization, VMD is much quicker.

Tutorials

• using VMD to display and manipulate '.pdb' files
• loading coordinate files into VMD with the help of an AMBER topology file e.g. to visualise the results of a GMIN run using AMBER9
• making moves from a '.pdb' file containing multiple structures. This is dealt with in the OPTIM section as part of the tutorial on making a movie of a path