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.

Coloring Method

Dynamic Color Code

When assigning color code to variables that change during the simulation, such as velocity, force, polarization charge, etc. If the variable you are trying to plot is not recognized by VMD, you could trick VMD by changing the corresponding comment line of that variable name to be "vx" (only need to be done for the first time step). Then, VMD will interpret it as x-component of atoms velocity.

Next, in the "Coloring Method" drop-down list under "Graphical Representations", choose "Trajectory"->"Velocity". This will use velocity amplitude as the color value. If "vy" or "vz" is not specified, they are zero by default.

To change the color scheme, go to "Graphics"->"Colors", under the "Color Scale" label, choose the appropriate method. The change made in color scheme here won't show immediately but in the next frame.

For example, in the RWB method, if the value range of your data is from 1.0 to 1.5 (You can set your "Color Scale Data Range" under "Graphical Representations"->"Trajectory" label), without offset, atoms with value close to 1.5 will be red, while close to 1.0 will be blue.

Note: The values for the color code are supposed to be positive. VMD takes negative value but only taking its absolute value. This becomes a problem if one has a set of data ranging -1.0 to 1.0 wishing to have -1.0 blue and 1.0 red. A trick one can do is by manipulating the dump file, add a global constant to all values (making every entry of that variable column positive), then shift the "Color Scale Data Range" also by that constant.

One color scheme applies globally to a whole "molecule". To have multiple color schemes for one molecule. Load the molecule multiple times, under the "Graphics"->"Representations" ->"Selected Molecule", do different schemes for different selection of atoms under different selected molecules.

Miscellaneous

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."