When you start to exercise your body starts to have physiological changes. You breath faster and more deeply, your heart rate increases and you start to shunt your blood supply from your abdomen to the muscles for a better delivery of oxygen.
These changes do not happen instantaneously, it takes a few minutes for your arterial and venal systems to dilate or contract to move the blood around. This period is typically what is referred to as the warm up. The length of time of your warm up should depend on factors such as your age and your current level of fitness. The older or more out of shape you are, the longer your warm up period should be. For most people 5 to 7 minutes should be sufficient.
Dynamic warm ups are the easiest way to get ready for exercise so start with movements similar to the sport you plan to do and slowly increase the range of motion and the explosive power until you're up to full speed. If you find you are fading towards the end of your workout, it is probably because you didn't warm up fully and this resulted in an increase in lactic acid in the muscles which causes fatigue.
All of this explains why the beginning of your run seems hard (you're still warming up) the middle part seems easier (you have a good delivery of oxygen to the muscles) and the end seems to get harder again as you increase the running time (fatigue).
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