Introduction to VMD software

VMD Main Menu and Renderer Window

• VMD program has two separate windows:

1. VMD Main Menu: Contains the toolbars for opening the files, changing representations, applying filters, and creating snapshots or movies.
2. Renderer Window: Shows all the rendering and visualization of the molecular and atomic structures.

Opening Molecular structures in the VMD software

• In the VMD Main Menu -----> File ----> New Molecule
• Load files for option is to load a new molecule or load a file and assign it the currently loaded molecular structure.
• Determine file type is usually set to Automatically in order to enable VMD software to recognize your file type based on its extension.
• Load button will load the selected file and the renderer window will show the basic visualization of your file.

Changing graphics representation

• In order to change representation of molecular structure in the renderer window, in VMD Main Menu go to Graphics ----> Representations
• In the Selected Molecule section you can choose which structure you want to change its representation.
• You can create multiple representation for a single molecular structure by using Create Rep and delete them by using Delete Rep.
• In the section that shows Style, Color, Selection:

1. Style: Shows which style or graphical representation mode is used for the current atomic structure.
2. Color: Shows which variable is used to color the chosen representation.
3. Selection: Shows which part of the molecular structure is chosen to create visualization.

• Selected Atoms: select specific parts of the molecular structure.
• In the Draw Style sub-section you can change the Coloring Method, Material, and Drawing Method:

1. Coloring Method: Shows the available variables for coloring the molecular structure.
2. Material: This option controls the rendering mode such as rendering as an opaque or transparent mode.
3. Drawing Method: This option controls the representation style of molecular structure such as rendering the atomic bonds as line or rendering the atoms as sphere, etc.

Changing selection type of the molecular structure

• In the same Graphical Representations window, if you switch to Selections section, you can select different parts of a molecular structure, such as its backbone, helixes, waters, etc.

Create Periodic Visualization of repetitive structures

• Some molecular structures such as crystals have repetitive pattern, but in molecular dynamics simulations only the smallest repetitive part will be simulated. On the other hand, for visualization of these kind of molecular structures you can bring back the periodic or repetitive pattern.
• Choose Periodic section of the Graphical Representations and add periodic image in +X, -X, +Y, -Y, +Z, or -Z directions.

high quality images based on different rendering engines

• There are some rendering engines in the VMD software, that could be used to produce high quality visualization images.
• Most popular rendering engines are OpenGL, Tachyon, POV-Ray, etc.
• Choosing the right rendering engine depends on your hardware as well as the quality of the final rendering that you need to have for your visualization.
• For creating high quality rendering, go to in the VMD Main Menu: File ----> Renderer

Changing background color and other display options

• To change background color: Graphics ----> Colors
• In the categories section choose Display.
• In the Names section choose Background.
• In the Colors section choose the color that you want, for example 8 white.