Hi @PRAMOD_PATEL,
First thing first, please have a look at the formatting guidelines and posting advice of the forum. It will help you format your post in a readable way and phrase you questions better to get relevant help.
That being said, the crack example is a simple atomic 2d model in which it is easy to turn off interactions. This is likely not the case of your system. Some comments:
There are no axes reference in your image so I assume the z direction is upward. Yet this makes your box a little short in the horizontal direction to study crack propagation, and your “tip” is already as long as nearly half the box.
Also If you are working with polymer molecules, simply deleting the atoms is weird to me in that it will affect the dispersity (molecules length distribution) of your system in unpredictable ways. If you’re not removing the whole molecule, you are basically cutting atoms out randomly in a large patch. I don’t know how realistic this is and can’t tell how this affects the system properties.
From what I see, I guess you are showing an Ovito picture with default color settings. From the low resolution picture, I see no yellow or purple atoms in your simulation. I would conclude that this commands actually does nothing useful in your case.
Overall, you are also performing a 3d NPT simulation with long molecules probably crossing periodic boundaries. So it is expected that the hole you create actually fills since it is surrounded by atoms. This is different in all ways from the crack example. So both are not comparable.