[gmx-users] per mol of what?

Ángel Piñeiro angel.pineiro at usc.es
Thu Sep 26 18:13:38 CEST 2013

when calculating an energy contribution using g_energy, the units
specified in the plots, as well as in the output tables, are kJ/mol.
This happens even when the -nmol flag is missing (so nmol=1). On the
other hand, the energy units in gromacs are kJ/mol. So I guess that when
a term (a dihedral or whatever) is added to the total potential it
refers to kJ per mol of that term. The total energy of a system comes
from the sum of all the potential energy plus the kinetic energy
contributions and the units are again kJ/mol. Then, how should I
understand that? kJ per mol of system contained in the unit cell?

Let me put an example: I have 6 solute molecules solvated in 5000 SPC
waters and I use g_energy to determine the coulombic contribution to the
solute-water interactions or to the solute-solute interactions as a
function of time. The result is given in kJ/mol. If I want to determine
the same contribution(s) per mole of solute should I divide by 6
maintaining the units as kJ/mol? Then, if I have the same system with 12
solute molecules, would make sense to compare the equivalent
contribution divided by 12? After taking a look to the code and to the
results for a couple of systems I think this is correct but the answer
is too basic and important just to assume that I am right so I would be
happy if I have a confirmation.

Thanks in advance,


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