There are many tools you can use for this. But all this is depend on your objectives. If you have some knowledge in python and its related packages such as numpy, pandas, matplotlib you can use MDAnalysis. The other widely used language for data analysis in computational biology is R. If you are familiar with R you can use Bio3D packages. Please see the links below,

https://www.mdanalysis.org/

http://thegrantlab.org/bio3d/

Indika Bandara Samarakoon thank you for your answer.

You can use MDAnalysis, MDTraj, or something built into your simulation software package to calculate what you are interested in. Then you can Seaborn. They have tutorials that show you how to plot histograms:

https://www.python-graph-gallery.com/20-basic-histogram-seaborn

To plot multiple variables like in the example your showed:

https://www.python-graph-gallery.com/25-histogram-with-several-variables-seaborn