[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,
Firstly, thanks for your reply.
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?
Thanks in advance
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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