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

[Alex]

I already answered your question. If you prefer words like "extensive 
thermodynamic property," please consider your favorite equations from 
thermodynamics, in which a linear function of energies, values of PV or 
TS are present. On the other side, despite the fact that all of these 
equations have been traditionally rescaled to 1 mol, there is total mass 
of the system, i.e. what you call "extensive thermodynamic properties" 
are nothing but properties of a given amount of matter.

The same logic explains the difference between total volume and volume 
per mole. Your energy of intermolecular interactions is ~ 170 kJ/mol.

Alex


On 8/26/2018 10:12 PM, Dhawal Shah wrote:
> 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>*