We will need to change Directory Root field according to first running store's installation folder. In this case, it is /public_html/store folder.
Let's complete adding subdomain by clicking on the Create button.
The next part of setting up second store involves using OpenCart Admin panel:
Let's browse into System | Settings menu.
We click on Create A New Store button on the top.
We fill all the needed fields on all tabs to customize the second store with vital information like Welcome message, localization settings, etc. The most important setting is the Store URL field in which we should write http://store2.yourwebsite.com.
Let's click to Save to finish.
Now, we should assign individual products, categories by editing each of them.
Let's remember that we can only run multiple stores on different domains or subdomains. So, it would not be possible to run another store on another subfolder such as http://yourwebsite.com/store2.