Respect user input for nstcomm

This replaces do_md overwriting ir->nstcomm by a warning at grompp time. Until now, nstcomm was set to the computed global communication frequency if nstcomm < nstglobalcomm. The user is now informed at grompp time that their choice is not optimal, but the set value is respected. The criterion for the warning now also encompasses any value for nstcomm that is not a multiple of the global communication frequency, since nstcomm=11, nstglobalcomm=10 is not much better than nstcomm=9, nstglobalcomm=10.

Resolves a TODO, and refs #3854 (closed).