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

[Alex]

The potential energy _of the system_ is reported, and that's directly 
proportional to the number of molecules you have in your box. Energy per 
mole is a unit regardless of the number of molecules. After you properly 
rescale the total energy with the number of molecules, you still get 
kJ/mol, of course. In one case, it was per the entire system containing 
N molecules, in the other it is per molecule. You do not weigh x kilos 
per Dhawal, you just weigh x kilos.

Alex


On 8/26/2018 9:02 PM, Dhawal Shah wrote:
> 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