Minimal VMD

VMD is a (bio) molecular visualization package with a lot of cool tools to do static and dynamic property predictions from MD trajectories. Though we could get by all the basic operations with GUI, there are few useful tricks that needs TKL console commands. I will detail a few important day-to-day commands here.

Transparent sphere

Sometimes we might need to draw a transparent sphere to represent atoms within a cutoff radius. This is not straight forward from GUI. The following commands does the trick.

draw material Transparent
graphics top sphere {x y z} radius 6 resolution 80

Set periodic boundary condition (PBC)

Visualizing periodic structures from an xyz file which is devoid of lattice information wants the missing information from the user to setup PBC. The following codes does it for you. The lattice info is given here in {x, y, z, alpha, beta, gamma} format. Tag '-all' sets it to all frames in the trajectory.

pbc set {7.6092 8.7863 24.3422 90.0 90.0 90.0} -all
pbc box