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
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