Hi Katerina
I had a look at your data files. Incidentally, VMD+topotools can view multiple data files at the same time (without needing to merge them beforehand). I looked at the two data files using VMD+topotools by selecting the “Extensions”->“Tk Console” menu option and entering these commands:
topo readlammpsdata system1.data atomic
topo readlammpsdata system2.data atomic
(Incidentally, if you want to merge the two data files, you can follow this with a “writelammpsdata” command. See the topotools documentation.)
It looks like the atoms in these two data files really are mixed together. My guess would be that whatever went wrong occurred long ago, before you created the system1.data and system2.data files. Not much at this stage we can do to fix it.
I suggest that you focus your efforts on building each system independently. Start with the simpler system (for example, the wall system). Try to build that system correctly, and check it visually using VMD+topotools to confirm that it looks correct. Once it does, then try building the other system (the polymer system). Once you have that working, then you can try combining them into one big system. Start simple. Then add complexity. It’s usually too tricky to try and do everything at once on the first try.
There is another problem: You should be using “atom_style molecular” (or preferably “atom_style full”). It seems like you are using “atom style atomic”. This will prevent you from including bonds in your system.
Andrew
(The early stages of setting up a molecular dynamics simulation are never fun.)