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

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 29 19:37:43 CET 2016


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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