Just spent the last five hours looking for this story!
Rodney/John in Atlantis. The boys have bad!sex and John demands a rematch. They begin sleeping together, but John (and maybe Rodney too?) is not sold on the idea of a relationship. They up the ante and just keep trying to impress the other person. In the end, they wind up frotting in a bathtub and they realize they've developed feelings for each other (or maybe they've had them all along?).
Possible/Might be a diff. story: Ronan puts his hand down John's pants--not a sexual thing but about connecting as warriors or some such craziness--and Rodney sees and gets jealous.