Knowing how to calculate distances and angles between points in three-dimensional space, and knowing Python, i would generate Python lists of the distances and angles, and plot them (as histograms) with MatPlotLib.

You can use ReaxFF (https://www.scm.com/product/reaxff/) to calculate bond-length and bond-angle probabilities as well as many other parameters related to chemical reactions in large-scale molecular systems. This is actually the software used to generate graphs in panel c and d of your figure.

There are many programs in which you can do this, but choosing the one that will make it easiest on you depends on what kind of trajectory file you have. What program did you use to generate the trajectory? If its VMD-compatible, like an mdcrd or dcd file, you can analyze the bond lengths quite easily:

https://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node5.html

Particularly step 13 explains how to display the bond length between these atoms - or any other pair - over time. Almost all popular trajectory file types can be opened in VMD, so this will likely work for you

you can perform your molecules through Gaussian and optimized structure log file contain bond length, bond angle, dihedral bond angle etc. hope so it will help you.

Mohammad Saeed Bahramy I got this software, could you please explain how can I extract them from a let's say single snapshot of a structure?

Ehsan Shahini

Please have a look at this tutorial (http://www.wag.caltech.edu/home/duin/Reax/Reax_training.pdf). This should help you out.