Dear All

I'm running MD with NVT ensemble, I started from a geometry optimized structure, then I ran a 50ps MD simulation with Andersen thermostat to relax the structure. After that, I ran 1000ps MD simulation with Nose thermostat (Q ratio = 0.01) for the equilibration, and another 1000ps MD simulation with Nose thermostat (Q ratio = 1) for the production. I observed big temperature oscilation (+- 15K) at the beginning of production, but damped out within 100ps. However, the kinetic energy for the whole production is very stable. I attached the temperature and energy curves for the production stage. Would the oscilation affect the data analysis?

Thank you.

Jingjing Bu