[gmx-users] potential energy per molecules or per mole

[Dhawal Shah]

Greetings!

I am confused about the units of potential energy in gromacs. I have
performed simulations of pure monoethanol (MEA) systems with certain
parameters. The three systems I simulated consisted of 2400, 2800, and 3200
molecules of MEA, respectively, at 298 K and 1 bar. After reaching
equilibrium, the potential energy of the systems (as computed from gmx
energy were)

Number of MEA molecules

MEA-MEA interaction energy (kJ/mol)

In pure MEA

2400

409523.0

2800

477119.5

3200

545348.3

How, can the potential energy (with units kJ/mol) be different for
different systems. It is all pure MEA, and the systems are in equilibrium.
Also the units is per mole. Energy per mole should be independent of the
number of molecules simulated?

However, if I divide the energy by the number of molecules, it is roughly
the same. 409523/2400 = 170.63; 477119.5/2800 = 170.39; 545348.3/3200 =
170.42. What is the unit now = kJ/mole/molecules?

If I want to understand the strength of interactions between MEA molecules,
should I choose 170 kJ/mol/molecules or 409523 kJ/mol?

Regards,
Dhawal