tMRD is specified in ns in Altera® High Performance(HP) DDR2 Controller and in terms of tCK cycles in Micron's device datasheet. You will convert tMRD to ns by multiplying the number of cycles speicified in the datasheet times tCK. tCK would be the memory operation frequency and NOT memory device's tCK.
For example, tMRD is 2 * tCK in micron datasheet. If the memory device can run at the top speed of 266MHz, the min tCK as specified is 3.75ns and if you are running the memory at 210MHz tCK for your implementation will be 4.75ns. So you would enter 2*4.75=9.5ns for tMRD parameter in the Megawizard®.