I read your questions carefully and most of them can be better
addressed by you carefully reading the documentation for fix nph (part
of fix_nh.html). If you do that, you will also learn a lot of other
useful stuff. It is true that 'energy yes' does not modify the
dynamics of the system. The reason why I set pchain=0 was to use
construct the simplest possible barostat. For a real simulation, it is
better to use pchain>0.