Save settings and visualization states

You can save your preferred setting for default VMD states in the file .vmdrc. VMD comes with a GUI editor for this file in the Main window under Extensions > VMD Preferences, which is generally the best way to customize the settings. Play around!

When you have a more specific visualization, perhaps a way to load a specific type of system consisting always of a topology system.psf and coordinates system.dcd, you could create all the desired representations, colors, materials, etc, then save the visualization state in Main under File > Save Visualization State… Save it as something like view_traj.vmd. Then load it later on using vmd -e view_traj.vmd. It is essential to spend time creating these save states early on in a project, and set them up so that you can load the saved state quickly and inspect your simulations quickly and visually!