Trajectory handler

Many simulations in EasyHybrid produce more than one set of coordinates: molecular dynamics, geometry optimizations with saved trajectories, reaction coordinate scans, NEB and umbrella sampling, as well as trajectories imported from files. Each of them is stored as an object of the system, with one or more frames. The Trajectory Handler (EasyHybrid Player) is the tool used to move through these frames and to play them as an animation in the 3D view.

To open the tool, click the Show Trajectory Handler icon on the main toolbar, or go to:

Main Menu > View > Show Trajectory Tool

The player is a small window that stays above the main window (Figure 1):

• Slider: shows the current frame and allows jumping to any frame by dragging it. Its range is updated to the number of frames of the trajectory being displayed.

• << and >>: go one step back or forward.

• > (play): plays the trajectory continuously. When the last frame is reached the animation runs backwards to the first frame and starts again (back-and-forth mode), until it is stopped.

• # (stop): stops the animation.

• FPS: the animation speed, in frames per second (default: 24).

• Step: the number of frames skipped at each step of the animation (default: 1). Larger values are useful to browse long trajectories quickly.

The frame shown in the 3D view is the same for all visible objects. Measurements done with the picking selection (distances, angles and dihedrals shown in the 3D view) are updated as the frames change. To analyze a trajectory quantitatively, see the tools in the Analysis menu, such as Distances, Angles and Dihedrals, RMSD tool and Align Trajectory.