[gmx-users] heat capacity in 4.5.3 and 4.0.7

[Elisabeth]

Dear all,

I am trying to calculate Cv of a pure alkane 125 molecules with actual
density, and here is what I have done:

1-


Cv: Run NVT > g_energy>select T and Etot=total energy

As I issue g_energy  *.edr

Heat Capacity Cv:      12.4787 J/mol K (factor = 0.000369503)



And when I choose –nmol XXX

Heat Capacity Cv:      13.4007 J/mol K (factor = 0.0462137)



- Do I have to use –nmol? What would be the unit with –nmol ?


and as I issue g_energy using 4.5.3


Temperature dependent fluctuation properties at T = 299.987. #constr/mol = 0
Heat capacity at constant volume Cv:    341.734 J/mol K


and with -nconstr # of bonds


Temperature dependent fluctuation properties at T = 299.987. #constr/mol =
19
Heat capacity at constant volume Cv:    262.746 J/mol K

- From this I am guessing what 4.0.7 reports is not correct!?


but still what I am getting from 4.5.3 is far from actual reported value
(around 170). I guess I am missing something..! or Is the difference
acceptable?



 g_energy says:

you will need to give the number of constraints per molecule –nconstr



- so I need to count how many bonds are fixed in the molecule as I am
setting constraints= all-bonds?

The way to this is counting no. of bonds?  What about macromolecules? Is
there an easier way of finding number of constraints?



2-


Cp:


I did NPT, g_energy *.edr -nmol XXX -nconstr  (4.5.3)

I want to select T and enthalpy but since enthalpy is not on the list I
select total-energy (which is Etot I think) and pv terms but g_energy is
still giving Cv!


Property                        Energy terms needed
---------------------------------------------------
Heat capacity Cp (NPT sims):    Enthalpy, Temp



Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Total Energy                86.1571      0.085    1.55565 -0.0944531
(kJ/mol)
Temperature                 300.074       0.07    5.77219   0.318146
(kJ/mol)
pV                          15.8128      0.061    1080.82  -0.249203
(kJ/mol)

Temperature dependent fluctuation properties at T = 300.074. #constr/mol =
19
Heat capacity at constant volume Cv:    325.067 J/mol K

Can you please guide me where the problem lies?

-------------------------------------------------------


again Cv : to compare with constraints=none

but still -nconstr should be on otherwise I values are more off.


Total Energy                132.418      0.051    1.77314   0.144794
(kJ/mol)
Temperature                 300.008      0.052    4.50209    0.15866
(kJ/mol)

Temperature dependent fluctuation properties at T = 300.008. #constr/mol =
20
Heat capacity at constant volume Cv:    442.016 J/mol K


3-

Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
Isothermal compressibility:     Vol, Temp
Adiabatic bulk modulus:         Vol, Temp


Since volume appears for calculation of the above properties , does this
imply only NPT results in these properties?

and wanted to make sure what 4.5.3 reports is reliable..


Many thanks for you time!

Best,
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