I begin by covering the stock until it reaches a steady simmer. After that I leave it partially covered for the duration, skimming off fat and proteins as they surface. I want it to be as clear as possible.
The classic method is to bring it to a boil with the lid on; a covered pot boils more quickly than an uncovered one. As soon as it comes to a boil, remove the lid, and adjust the heat to a simmer. Stocks should be simmered without a lid because you are simmering away water so as to concentrate flavors. Be sure to taste it at the 90 minute mark. There is no magic time for simmering a stock. It is done when it has reached a flavor concentration which pleases you.
Covering dilutes the broth a little, but you'll keep the same amount of liquid. I prefer a fuller flavored broth, so I don't cover mine or, I partially cover it. It really depends what your goal is.
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