6.23. Animation display area

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.

It is also possible to analyze results directly from this function for animated (trajectory) data, check Options ‣ Tools for details.

Reload

Re-load the animation file.

Options
Export
Current Frame

Saves the current frame as a different name.

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.

GIF Animation

Write a GIF animation file.

You can also operate from the Export button.

JPEG Images

Export serial number JPEG file.

You can also operate from the Export button.

MOL2 File (Multiframe)

Writes out a mol2 file containing all frames.

SDF File (Multiframe)

Outputs all the frames to a separate file.

WMM File (Multiframe)

Writes out a WMM file containing all frames.

Animated GRO File

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

CSV

Outputs the numbers displayed in the list in csv format.

Tools
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.

Append Trajectory

Connects animations from other files to the current animation. This is useful when you want to join trajectories of forward and reverse IRC calculations around a saddle point.

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.

Displacement of Selected Atoms
Extract Trajectory for Selected Group

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

Auto

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.

Enable Dynamic Bond

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.).

Speed

Adjust the playback speed.

Loop

If it is checked, the loop will be played.

Open Viewer

Display the currently open animation using Winmostar Viewer.

Frame

Manipulate and adjust the display position.

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.

Custom Plot

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