In my long runs (about 25k) when I finnish the smell of my body is like ammonia, I have read in internet thats because of converting my muscles into energy, so Could I say that my body is not burning fat like it should be? the other question I would like to ask is, How do I know when my body is burning fat correctly? I mean there is some indicator? like the ammonia smell is to burning muscles?
The ammonia smell is caused by your body using protein as a fuel source. When necessary, the body will turn to breaking down protein to get glycogen, and the waste products can over load the mechanisms for getting rid of them. When this happens, one of the pathways for excretion is through sweat, and ammonia is one of the waste products.
This will generally happen when on a high protein, low carbohydrate diet.
Your body is always burning both fat and glycogen. At lower intensities, the mix will be fairly balanced between fat and glycogen being used for energy, as the intensity increases you will tip more towards the glycogen end of things, but fat is never cut out of the equation.
Also, if you do long duration training, you may get the ammonia smell anyway, as you have pretty much depleted your bodies ready glycogen stores (Muscle and liver).
In general it is thought that your body takes three approaches to energy sources while exersizing.
If your percent heart rate (HR) is below 80% usually people will be burning fat. If your HR gets higher, your body will switch to using glycogen for fuel, since it can be processed faster.
Eventually you can burn muscle, but that is usually pretty extreme.
I too find an ammonia like smell, and have just accepted it is the cost of distance running.