Clean up gmx_mdrun()
NFILE is inconsistent with usage in the rest of mdrun, changed to
nfile.
Removed outdated comment.
Changed several variable names to *_choices, because in two cases the
actual selection gets passed to runner() as a pointer to the updated
first element of the choices (which is organized by
parse_common_args()). It's easier to understand that the variables
have different roles in the two places if they have different names.
Renamed nstlist and nsteps to the same with the _cmdline suffix that
is used in mdrunner().
Change-Id: Id99fa26b7ab38cd67de8f259c612179ad7f1e992