Read the ruling. If they don't sort it out themselves in 45 days, the judge will impose an ongoing royalty rate. The only reason he didn't do it already is to preclude an appeal by Apple.
Judge Davis in the Eastern District of Texas, who oversaw the jury trial that awarded $368.2 million to VirnetX for Apple's infringement of VHC's patents with FaceTime, confirmed the jury's verdict today in a 47 page ruling, with interest and ongoing damages of $330,000 per day. He also chose not to set an ongoing royalty rate, rather he ordered the parties to come to a settlement themselves via mediation on an ongoing royalty rate for Apple to pay VirnetX for continued use of its patents, and said that if they failed to do so within 45 days, he would impose one. Separately, he essentially confirmed that VHC's damages expert had submitted "substanital evidence" that 1% of infringing revenues was a reasonable royalty - making it clear that if the parties didn't agree within the next month and a half, he'd impose that rate on Apple. Depending on which products qualify (essentially anything using iOS or OSX), that would be somewhere between $500 million and $1 billion a year, or 1-2% of AAPL's net income. Should be an interesting 6 weeks.