atoms stick together badly

I try to simulate solid porous organic cage (CC1) with C, N and H atoms. but when I run nve and then npt and visit the result in VMD, atoms stick together badly.

Is problem from input (potential parameters) or from VMD or from initial molecule?
If my input is incorrect, can you help me to correct that?

poc.in (3.44 KB)

I try to simulate solid porous organic cage (CC1) with C, N and H atoms. but when I run nve and then npt and visit the result in VMD, atoms stick together badly.

Is problem from input (potential parameters) or from VMD or from initial molecule?
If my input is incorrect, can you help me to correct that?

Debugging and correcting an input for a simulation software is a skill that every computational scientist should have. I suggest you have a discussion with your adviser / supervisor how to acquire it. Typically this requires practicing with smaller, simpler systems, comparing to text books and validation data, and manually comparing input to expectations.

Axel