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

[David van der Spoel]

On 29/01/16 19:54, Alexander Alexander wrote:
> 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"?
By selecting -nmol 10976 you are defining what the molecule is.
>
> Also, no comment please about strange behavior of the Cv-T?
This is not strange, it just warns you to check whether the simulations 
have converged. If not the cV you measure is in fact the drift in the 
energy. So plot your energy and make sure it is converged.


>
> 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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-- 
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