As mentioned in the title I want to trace the dynamic of an atom from an AIMD trajectory. Is there any tool to visualise it ?. I want something like the attached figure.
I think you can write a python script for yourself, because most of MD visualization software designed to deal with large number of atoms, to save memory, they only load one configuration at time. I don't know how about QM software.
I recommend VPython library, it's easy to use so you can freely customize your own code