Updated to use gmx executable.

Changed the logic to use the gmx[_mpi][_d] executable and to
use the gmx check program. In addition use of the -prefix option
is deprecated. Added a new -mdrun command to allow running
non-default mdrun commands. Added a new -mpirun flag to allow
selecting yet another mpirun command. Removed the -mpiforall
option.

Change-Id: I8ca55355280fd67c8ee03d3a79d261d7d032d19a