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

Ahmet yıldırım ahmedo047 at gmail.com
Tue Apr 16 09:29:07 CEST 2013

```Dear Prof. Spoel,

I looked at the paper your said.
1.) To calculate the density d in a constant pressure simulation (in npt
simulation):
d=M/<V> equation (5)
M: mass of the system
V:volume of the system
Doesnt this formula (equation 5) use when Gromacs calculates the density of
system?

2.) The classical-that is, without any quantum corrections-heat capacity cP
can be obtained from the fluctuations in the enthalpy (from your paper):
cP=<H^2>/(kB.T^2) (equation 13)
How did you calculate <H^2>?

3.)You said before "
http://www.mail-archive.com/gmx-users@gromacs.org/msg37580.html"
cP = (<H^2> - <H>^2)/kB T^2 (NPT sim)

This formula doesn't equal to equation 13. There isnt <H>^2 term in
equation 13. Why?

2013/4/12 David van der Spoel <spoel at xray.bmc.uu.se>

> On 2013-04-11 22:20, Ahmet yıldırım wrote:
>
>> could anybody help me please?
>>
> Check http://pubs.acs.org/doi/abs/**10.1021/ct200731v<http://pubs.acs.org/doi/abs/10.1021/ct200731v>
>
>
>>
>> 2013/4/11 Ahmet yıldırım <ahmedo047 at gmail.com>
>>
>>  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<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
>>>
>>>
>>
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
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--
Ahmet Yıldırım

```