Plotting and visualizing collective variables

Timeline plots show the selected variables as a function of time. A vertical bar indicates the current frame, which can be changed either using VMD's trajectory animation controls, or directly in the plot window by clicking the mouse inside the graph, or using the keyboard left/right arrows. Shift+arrow skips frames for faster animation, and Ctrl+arrow skips more frames. The up/down arrows operate a zoom/unzoom along the time axis. Visible data can be fitted vertically using the h key. All data can be fitted horizontally using the h key.

Pairwise scatterplots are useful to identify correlation between variables. To create a pairwise plot, select exactly two scalar variables (or scalar components of vector variables), and click ``Pairwise plot''. Frames are represented by circles, and lines connect consecutive frames. The blue dot tracks the current frame. Arrow keys animate the trajectory as in the timeline plot. Clicking a circle jumps to the corresponding frame.

``Show atoms'' creates representations of the atoms involved in the definition of the selected colvars. Each atom group is shown in a different color. ``Show gradient'' is available for scalar variables only. It creates a graphical representation of the atomic gradients of the selected variables, visualizing how the value of the collective variable would vary in response to a change in atomic coordinates. Vectors representing the gradient are rescaled as indicated by the radio buttons Set max. vector norm and Set scaling factor. Set max. vector norm rescales gradients so that the largest vector component of each colvar's gradient is represented by an arrow of the specified length, in Å. Set scaling factor rescales gradients by the specified factor, divided by the colvar's width parameter (1 by default, see ). This use of width makes it easier to compare the gradients of collective variables that are not commensurate. The scaling factor has the unit $\AA * L / (cv / width)$ , where $L$ is the current length unit, and $cv$ represents the natural unit of the collective variable. By default $width$ is unity, but $(cv / width)$ may be seen as dimensionless if $width$ is expressed in cv units.