When using “gmx energy” to calculate the molar enthalpy H and the temperature T, with option “-fluct_props”, we obtain the molar heat capacity c_p. I have two questions about this output c_p.
How do GROMACS calculate the molar heat capacity c_p from the molar enthalpy H and the temperature T? Is it by this equation?
N = number of molecules [dimensionless]
and the gas constant
- Inconsistency with the physical equation?
By physical definition, the molar heat c_p is derived from the heat capacity C_p as
Thus, to put it physically accurate,
, thus; and.
where N = number of molecules [dimensionless].
Assuming that the equation I proposed in the first question is correct, then comparing it with the equation of c_p in my second question, there is apparently an inconsistency.
GROMACS mentioned that “There is no distinction between Boltzmann’s constant k and the gas constant R…” (GROMACS Documentation, Release 2019, section 5.3.2 MD units, p. 300, http://manual.gromacs.org/documentation/2019/manual-2019.pdf).
But by physical meaning, they are different. I cannot make sense of it, and get stuck at this inconsistency. May someone please help explain?
Thanks a lot, in advance!
I’d greatly appreciate your guidance.
Anh T. Mai