lammps-users Digest, Vol 107, Issue 99

To check the periodic boundary conditions you may just to visualize your files using VMD or other tools,
you can see here how it is done in my blog:
for your case you when you load VMD you will need to use this command instead:

topo readlammpsdata here_comes-<atomic>_or<full>
animate write psf traj.psf

As for simulation textbooks you may look into some workshop presentations:
then if you find something interesting just google it probably you will find something interesting on the Lammps mailing list.

Or just study lammps example files.

PS Siavash, make sure next time you reply you CC the lammps mailing list.