One way to do it would be

1: to run classical molecular dynamics, fixing the pressure (e.g. 1 bar) and temperature (T = 10,...,300K) using a NPT integration of the equations of motion for very long times, and then

2. take the average of those parameters over time.

Dear Fernan Saiz,

Thanks for your answer.

I performed 5000 steps MD calculations. How can I get average structure from the 5000 structures in MD result?