6.24. Animation operation 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 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.
- JPEG Images
Export serial number JPEG file.
You can also operate from the Export button.
- XYZ File (Multiframe)
Writes out a xyz file containing all frames.
- 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.
- CSV (Values)
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.
- Mean Square Displacement/Diffusion Constant
Calculates 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 may provide an equivalent function in the solver’s menu. Some solvers will ask you how many steps each frame of the animation is output every other step and the time per step of the simulation (time ticks, delt t). If you are not sure of the value you entered, check the maximum value on the horizontal axis of the displayed mean-square displacement and if it matches the simulation time, you are good to go.
- 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
- Change in Number of Molecules for Each Molecular Species
Plot the molecular number change for each molecular species.
- Rotational Autocorrelation Function
Calculate the rotational correlation function using the Legendre polynomial P2 of the second degree of the vector defined between the two atoms. The first vector is defined between the first and second atoms of the group to be analyzed, the second vector between the third and fourth atoms… The object of analysis is determined in the following way The average of the rotational correlation function for each vector is plotted.
- Intramolecular Vector Autocorrelation Function
Calculate the autocorrelation function of vectors defined between two atoms. The first vector is defined between the first and second atoms of the group to be analyzed, the second vector between the third and fourth atoms… The object of analysis is determined in the following way The average of the autocorrelation function for each vector is plotted. It can be used to obtain the end-to-end vector autocorrelation function of a polymer.
- Draw Path
The trajectory of each atom in the selected group is displayed as a line in the molecule display area.
- 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 . 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.