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.s...@nu.edu.kz <dhawal.s...@nu.edu.kz>* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.