I set my t_start and t_stop as 0.52 (lj unit), and I ran the nvt first.
after it reached equilibration I ran the nve but found the temperature of the last 1000steps went up to 0.56 while my coworker still had the normal result around 0.52. 
we even used the same code but our results are quite different. why does the average temperature vary so much from the one I set before?
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$\begingroup$ my understanding is that initializing a stable thermal equilibrium in MD is very difficult, so a common practice is to start out with something, let it run, then reset the system energy to the correct thermal level you want $\endgroup$– helloworld922Mar 19 at 1:32
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$\begingroup$ You will have to be more descriptive in what you are trying to do. I have no clue what software system it is you are using, and your question does not contain a description of what your goal is and how the results differ from your expectations. $\endgroup$– Wolfgang BangerthMar 19 at 17:43
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$\begingroup$ What happens to the total energy of the system? Does it remain close to being constant even from before the last 1000 steps to the end? $\endgroup$– Juan M. Bello-RivasMar 19 at 22:53
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