Specifying path for a molecule transport along a protein

Hi,
I want to try SMD simulation to transport molecules along a protein channel. can anyone provide me some informative tutorial links for the same. In NAMD one can usually use hydrogen bonds of channel lining residues as reference for transport path . How can i do that in gromacs if i have to check transport of an ion across transporters lets say.
Thankyou for your time and suggestions.