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Well as far as I know, warm ups and cool downs are a bit of a mixed pot, some people don't do anything.
Personally I think a slow jog for 5 minutes or so with some bum-kicking/high-knee steps and long strides is perfectly suitable as a warm up, when it comes to a cool down though some really long sustained static stretches work really well for me. Stretching everything I possibly can! Obviously if you do this you have to be careful that you're doing the stretch correctly, there's quite a lot on the net about this, pics and descriptions and so on, and obviously that you don't overstretch because this could cause the muscle to tighten up in response... which is the opposite to what you wanna do.
I also do yoga, and incorporate some of the poses post-run, especially the kneeling ones as I don't know how else to stretch my ankles and feet. The class I go to once a week just happens to fall right after my speed-work run at the gym heh. But there's also a really good book called "yoga for runners" by Jean Crouch which I use when I do yoga at home. Increasing your flexibility (if done right) can be really good for protecting against injuries, fight against tight muscles and build up strength in specific muscle groups. That book has a routine for pre- and post-running.
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