How to plot a trajectory for Li-ion diffusion in a crystalline Li-ion conductor ?

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Ponniah Vajeeston

Hi!

Here are the general steps to use VMD to plot the trajectory of Li ions in LiCoO2:

Load the simulation data into VMD: You can load your AIMD simulation data (coordinate and velocity files) in VMD using the "File" -> "New Molecule" menu option. You can also load the data using a TCL script.

Visualize the structure: Once the data is loaded, you can visualize the structure of the LiCoO2 using the "Graphical Representations" menu option. You can choose different representations, such as "lines" or "balls and sticks" for the atoms.

Plot the trajectory: To plot the trajectory of the Li ions, use the "Trajectory" menu option and select "Play Trajectory". You can also use the "Trajectory" -> "Load Trajectory" option to load the trajectory data and then "Trajectory" -> "Play Trajectory" to visualize it.

Customize the visualization: You can customize the visualization by changing the color and size of the atoms, adjusting the camera angle, and adding labels or other visual elements.

Save the visualization: You can save the visualization as an image or movie file using the "File" -> "Save Snapshot" menu option.

Dr. Sambath Baskaran

Hi..

I have made these two videos for VASP AIMD calculations. First video i have explined how to convert XDATCAR to .pdb file and next one I explained how to make movie from XDATCAR.pdb file. If you discover this information to be beneficial, kindly express your support by giving it a thumbs up, leaving a comment, and sharing it with others. We appreciate your viewership.

How to Convert AIMD XDATCAR file into a pdb file using VASPKIT: https://youtu.be/zYopurMg0Ac?si=vgaAjQCxJ72_G6p3

How to create a movie from XDATCAR file: https://youtu.be/x987ZKr5GB4?si=dFHf0Usq4wItNQ1q

Thank you

Best