Dear Andrew,
Many thanks for your kindness.
I already have further idea about the simulation. Actually, there are many ways for thermostatting including Langevin, temp/berendsen and ttm. The following reference shed some lights on these techniques. Thermo skin is a structure people normally use.
http://www.sciencedirect.com/science/article/pii/S0168583X0500813X
However, I am still thinking how to figure out a good thermo skin volumn.
Regards,
Ben