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:
http://bazilevs31.github.io/using_vmd.html
for your case you when you load VMD you will need to use this command instead:
topo readlammpsdata traj.data here_comes-<atomic>_or<full>
animate write psf traj.psf
As for simulation textbooks you may look into some workshop presentations:
http://lammps.sandia.gov/workshops.html
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.
Cheers,
Vasiliy