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

[David van der Spoel]

On 2013-04-11 22:20, Ahmet yıldırım wrote:
> could anybody help me please?
Check 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
>>
>> 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