Made g_tune_pme work correctly again with thread-MPI mdrun

Made g_tune_pme work correctly again with thread-MPI mdrun

Up to now, g_tune_pme would put the -nt switch on the mdrun command
line to ask for thread-MPI processes. Due to changes in mdrun, this
now leads to the fact that all runs with separate PME nodes exit
because the number of MPI threads must be explicitly specified with
the -ntmpi switch. Now the g_tune_pme -nt option is renamed to -ntmpi.
The remaining changes are only minor code cleanup / formatting things
plus getting rid of unused variables.

Change-Id: I7518799ef593d78d1cce1496852f0241e6d01755