# [gmx-users] thermal conductivity,specific heat,enthalpy

Ahmet yıldırım ahmedo047 at gmail.com
Thu Apr 11 09:35:43 CEST 2013

```Dear users,

I calculated diffusion constant of a substance using g_msd tool.  I also
want to calculate thermal conductivity its. By the way,I did npt simulation.

Diffusion constant=alpha
Thermal conductivity=k
specific heat=Cp
density=d
alpha=k/(d.Cp)
and
k=alpha.d.Cp
I need d and Cp to calculate k.

1.) To calculate Cp:
Prof. Spoel:From
http://www.mail-archive.com/gmx-users@gromacs.org/msg37580.html

cP = (<H^2> - <H>^2)/kB T^2 (NPT sim)

The .edr file gives average enthalpy <H>. According to above formula, I
need both H and <H>. How can I get H (not average)?
2.) .edr file:
1  LJ-(SR)          2  LJ-(LR)          3  Coulomb-(SR)     4
Coul.-recip.
5  Potential        6  Kinetic-En.      7  Total-Energy     8
Temperature
9  Pressure        10  Box-X           11  Box-Y           12
Box-Z
13  Volume          14  Density         15  pV              16
Enthalpy
17  Vir-XX          18  Vir-XY          19  Vir-XZ          20
Vir-YX
21  Vir-YY          22  Vir-YZ          23  Vir-ZX          24
Vir-ZY
25  Vir-ZZ          26  Pres-XX         27  Pres-XY         28
Pres-XZ
29  Pres-YX         30  Pres-YY         31  Pres-YZ         32
Pres-ZX
33  Pres-ZY         34  Pres-ZZ         35  #Surf*SurfTen   36
Mu-X
37  Mu-Y            38  Mu-Z            39  T-System        40
Lamb-System
Firstly I calculated Entalphy (16)
Afterward I calculated both Etot (7) and pV (15)
Enthalpy=Etot+pV
Unfortunately, I get "Enthalpy isnt equals to Etot+pV". Why?

--
Ahmet Yıldırım

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