[gmx-users] Heat capacity (C_{v}) for a solid

[Alexander Alexander]

Thank you so much for your response.

Concerning to the "-nmol"; this is also what I though that number of B is
the -nmol as whe have A3B , but do not you think that the number of
molecules depends strongly on how molecules or residuals are defined in the
topology file in [ moleculetype ] section? That is why I brought part of my
topology file above. If I had something like
------------------------------
[ moleculetype ]
; Name            nrexcl
   A3B                       1

molecules ]
;mol_name number
    A3B     43904
------------------------------
then you are right and the -nmol was (#A3B/4), but ... .

I am still wondering if the the Cv here is molar one as unit of it is
"J/mol K"?

Also, no comment please about strange behavior of the Cv-T?

Best regards,

Alex

On Fri, Jan 29, 2016 at 7:37 PM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 29/01/16 19:00, Alexander Alexander wrote:
>
>> Dear Gromacs user,
>>
>> I am trying to calculate the heat capacity at constant volume (C_{v}) in
>> different temperature for a solid structure with "A_{3}B" chemical
>> formula.
>> To do so, I made a big supercell containing totally "43904" atom by
>> keeping
>> the rate (#A = 32928 and #B=10976), below is a part of my topology file.
>> topol.top:
>> -------------------------------------
>> [ moleculetype ]
>> ; Name            nrexcl
>>    A                       1
>>
>> [ moleculetype ]
>> ; Name            nrexcl
>>    B                        1
>>
>> [ molecules ]
>> ;mol_name number
>>     A    32928
>>     B     10976
>> -------------------------------------
>>
>> After convergence of the MD simulation I invoked the below command:
>>
>> "gmx energy -f case.edr -nmol 43904 -fluct_props -o case.xvg"
>>
>> My first question:
>> what exactly I should use as "-nmol" in this specific case as explained
>> above? If it is (#A) or (#B) or (#A+#B)?
>>
> Since your formula is A3B I guess the number of "molecules" is the same as
> the number of B particles.
>
>
>> Second question:
>> I was wondering if the Cv printed out in screen after choosing "Total
>> Energy"  and "Temperature" in gmx energy is relabel?  At least in this
>> level as I know the Quantum part has not been included yet.  Or I have to
>> do the temperature numerical derivation of Total energy myself as
>> Cv=d(U)/d(T).
>>
> This is safer. Do the simulations at two or three temperatures and compute
> cV = dU/dT if constant volume or cP = dH/dT if constant pressure.
>
>
>
>> WARNING: Please verify that your simulations are converged and perform
>> a block-averaging error analysis (not implemented in g_energy yet)
>> Heat capacity at constant volume Cv   =    200.779 J/mol K.
>>
>> Third question:
>> If this is Molar heat capacity, am I right?
>>
>> The last:
>> Below are the result of Cv in different temperature for this system:
>>
>> (Cv  J/mol K) ----- (Temperature K)
>> 37037.700                      10
>>       200.779                      50
>>         40.497                      75
>>       124.360                      100
>>       321.416                      150
>>       620.247                      298
>>
>> I know these Cv do not include any corrections for quantum yet, but still
>> I
>> am puzzled about the strange behavior of  Cv versus temperature, I would
>> be
>> so thankful if one could explain it for me.
>>
>> (Version of Gromacs : is 5.1-rc1)
>>
>> Sincerely,
>>
>> Alex
>>
>>
>
> --
> 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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