Wait, I think this is the fic I was thinking of:

Forty-Two (5955 words) by cathalin
Chapters: 1/1
Fandom: Stargate Atlantis
Rating: Explicit
Warnings: No Archive Warnings Apply
Relationships: Rodney McKay/John Sheppard
Characters: John Sheppard, Rodney McKay, Jennifer Keller
Additional Tags: First Time
Summary: Maybe John has been paying more attention to Rodney than he's realized. Rodney does some thinking, and then tests a hypothesis.