6.24. Animation window

In the list on the left side of the window, the number of steps, energy, power, etc. of each frame are displayed. Clicking each line in the list will display the frame corresponding to that line in the main window.

At the bottom of the window, the values of the selected column in the list are displayed in a graph Column pull-down menu.

About animation (trajectory) data It is also possible to analyze results directly from this window. For details, please refer to the Tools menu.

File menu

Realod

Read the animation from the original file again.

You can also operate from the Reload button.

Export Current Frame

Saves the current frame as a different name.

Export All Frames Separately

Outputs all the frames to a separate file.

For example, it is useful when you want to divide the molecular structure of an SDF file into individual files and save and edit them. To re-aggregate split files into SDF files, use Aggregate multiple files into SDF format.

Export GIF Animation

Write a GIF animation file.

You can also operate from the Export button.

Export JPEG Images

Export serial number JPEG file.

You can also operate from the Export button.

Export SDF File

Outputs all the frames to a separate file.

Export Animated GRO File

Output animation gro file. It can be used for linking with VMD etc. You can also operate from the Export button.

Export CSV File

Outputs the numbers displayed in the list in csv format.

Close

Close this window. To reopen it, select Window menu ‣ Animation.

You can also operate from the Close button.

Control menu

Go to First Frame

Move to the first frame.

You can also operate from the buttons in the window.

Play/Pause

Play/pause the animation.

You can also operate from the buttons in the window.

Go to Last Frame

Move to the last frame.

You can also operate from the buttons in the window.

Tools menu

Invert Trajectory

Invert the trajectory. This is useful when you want to combine trajectories for forward and reverse IRC calculations around the saddle point.

Skip Frames

Thin trajectories are thinned at regular intervals. This is useful when you want to reduce the size of long trajectories and reduce the processing speed of the analysis.

Translate All Atoms

Translate every atom in every frame. This function is useful when you want to fine-tune the position of an atom when visualizing calculated data.

Set Origin as Lower Bound Edge of Cell

Set the starting point in each direction of the simulation cell for each frame to the origin. This feature is useful in combination with the Translate All Atoms feature.

Distance/Angle Change

Analyze the bond length, bonding angle, dihedral angle between specified atoms in the trajectory.

1. On the Bond/Angle Change window, select: guilabel:` Type`.
2. List the atoms that define the bond length, bond angle, and dihedral angle you want to calculate in Target Atoms separated by commas. Clicking Set button you can automatically enter atoms with markers in the main window.
3. In Plot, choose whether to output time change ( Time Change ) or histogram ( Histogram ).
4. Click the Draw button.

Mean Square Displacement/Diffusion Constant

Calculate mean square displacement and self-diffusion coefficient. See Diffusion Constant/Mean Square Displacement for details. Some solvers such as Gromacs do not enable this menu, but equivalent functions may be provided in the solver menu.

Radial Distribution Function

Calculate the radial distribution function. See Radial Distribution Function for details. Some solvers such as Gromacs do not enable this menu, but equivalent functions may be provided in the solver menu.

Extract Trajectory for Selected Group

In the main window, create a trajectory file extracting only the atoms selected from the group.

Automation menu

Operates on the structure of each frame when executing file output functions such as File ‣ Export All Frames Separately. The operations are performed in the menu sequence.

Check All/Uncheck All

Check/Uncheck all items from Deleting Hydrogen to Quick Optimization.

Deleting Hydrogen

Removes a hydrogen atom from the structure of each frame. This is equivalent to Delete All Hydrogens.

Extracting One Molecule

For each frame structure, only one molecule is left in the structure.

Adjusting Coordinate

Automatically adjusts the bond length for each frame structure. The same operation is performed as Adjust All Bond Lengths.

Adding Hydrogen

Hydrogen is automatically added to each frame structure. This is equivalent to To all atoms.

Quick Optimization

Performs a simple structural optimization for each frame structure. This is equivalent to Quick Optimization

Running MOPAC

Execute MOPAC for each frame structure.

Up/Down slider

Drag to move between frames.

Speed slider

Adjust the playback speed.

Loop check box

If it is checked, the loop will be played.

Dynamics Bond check box

Automatically generates joins for each snapshot every time.

It is useful for MD calculations in which chemical bonds are recombined (first principle MD, CPMD, ReaxFF, DCDFTBMD, etc.).

Open Viewer button

Display the currently open animation using Winmostar Viewer.

Export button

This is a shortcut for the menus under File.

Close button

Close this window.

Plot Column

Specify the columns to be displayed in the graph display section at the bottom of this window. You can also enter a value directly.

Excel button

Opens a window where you can flexibly plot list contents, interatomic distances, angles, lattice constants, etc.