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

[Dhawal Shah]

Dear Alex,

Thank you for your response. I agree with all your statements.

My issues are with units. In the first case, should it be kJ (total
energy), as it is the Total potential energy_of the system_? Total energy
of the system is an extensive thermodynamic property.

I mean, for example, volume. We have total volume of the system and volume
per mole. Both are different. If I say that 100 moles of water have 1000 m3
(Total volume_of the system_), and per mole, it is 10m3/mol. One is
system-size dependent and second one is not.

Regards,
Dhawal





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
*Dhawal Shah*


*Assistant Professor*
*Chemical Engineering Department*
*Nazarbayev University, Astana*

*Phone: +7 7172 70 9130 (O)*
*email: dhawal.shah at nu.edu.kz <dhawal.shah at nu.edu.kz>*