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):

-(dE/dV)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.