VMD

Overview

VMD is

Atom Selection

Under the "Graphics"->"Representations", one can create multiple layers of representations. Each layer is independent and has its own user-defined drawing style, coloring and section of atoms.

Under the "Selections" label, one can select atoms based on the attribution keywords of the atoms. For example, in the "Selected Atoms" input, uses can write

index >= 100 and vx <1.5

This will select atoms with atom-id larger or equal to 100 and x-velocity smaller than 1.5. This command supports logical operators.

3D Projection

Under the "Display" category, one can switch between "Perspective" (default) and "Orthographic" (recommended) views.

"Orthographic is commonly used in engineering as a means to produce object specifications that communicate dimensions unambiguously, each line of 1 unit length (cm, meter..whatever) will appear to have the same length everywhere on the drawing. This allows the drafter to dimension only a subset of lines and let the reader know that other lines of that length on the drawing are also that length in reality. Every parallel line in the drawing is also parallel in the object.

If you are looking at a larger scene with buildings then orthographic rendering gives a clearer measure of distance between buildings and their relative sizes.

With perspective mode lines of identical real-world lengths will appear different due to fore-shortening. It becomes difficult to judge relative dimensions and the size of objects in the distance."