Newbie question: how to relate MD results to thermodynamic derivatives?

Hello everyone:

I’m a molecular dynamics newbie, so apologies in advance for what is probably a very basic question.

I would like to use output from NPT molecular dynamics simulations in thermodynamic calculations that are part of a wider project. I have a file that has the following columns: temperature, potential energy, and kinetic energy. I need to calculate (where “d” is a partial derivative and “T” is a subscript meaning at constant T):

I don’t understand how to do this based on the data I have.

For example, temperature is not really constant in my NPT simulation. There is a thermostat, so it fluctuates. Also, how do I define the derivative? Is “dE” the value at one time step - the value at the previous time step? If anyone knows of any online resources that deal with this, I would appreciate any suggestions. Thank you.

The science that relates microscopic data to thermodynamics is called statistical mechanics (or statistical thermodynamics). If you want to do meaningful MD simulations, you would have to get a corresponding text book anyway. So that is where I would start looking. Axel.