Daniel,
Let me give you two good reasons to read a good book on molecular dynamics
or find someone who will teach it to you in person. You might even want to
throw in some statistical mechanics for good measure.
Equilibrium is not as simple as having constant temperature and energy.
This it reason one!
You don't know the difference between "fix nvt" and "fix nve+velocity
rescaling". Let me tell you right now: the difference is huge! This it
reason two!
Good luck.