Fixed mdrun_mpi detection for Gromacs 5.0

[peterkasson]

This seems a bit kludgy, but it's only weird in one case (gmx_mpi exists and mdrun_mpi exists). I've now found at least two major HPC systems (stampede, archer) where gmx exists and is thread_mpi, mdrun_mpi exists and is real MPI, and mdrun exists and is thread_mpi. This patch fixes the "no mpi executables" error in that case.

[peterkasson]

A few commits in here (trying to separate). Two major topics and one minor:

1. Fixing gromacs command names so Copernicus can handle Gromacs 5.1
2. First stage of refactoring cpcc to allow function calls from external Python as well as command-line

Minor: some tutorial bugs.

[peterkasson]

Added more patches to run with Gromacs 5.1.