[gmx-users] Fwd: C_v and Temperature

[Alexander Alexander]

No comment please?


---------- Forwarded message ----------
From: Alexander Alexander <alexanderwien2k at gmail.com>
Date: Thu, Feb 4, 2016 at 1:27 PM
Subject: Re: [gmx-users] C_v and Temperature
To: gmx-users at gromacs.org


Thank you for your response.

I am trying to calculate the heat capacity at constant volume for a crystal
solid in different temperature; below are what "gmx energy -fluct_props
..." gives me in 4 different temperatures:

T = 29.9    Cv = 24.4681 J/mol K

T = 99.9    Cv = 24.6643 J/mol K

T = 297.9  Cv = 24.4926 J/mol K

T = 799.9  Cv = 24.5054 J/mol K

And "gmx dos" gives something around "Heat capacity 0.000683396 (J/mol K)"
as quantum correction for all the simulation temperature I have tried.

The result for the two last temperature is fascinating and agree well with
my DFPT and phonon calculations as well as all the heat capacity laws in
higher temperatures.
Also, I was expecting that the C_v reduces to around 2 or 3 J/mol K  in
lower temperatures, but I do not know why the C_v in lower temperature is
the same as higher temperature, although I had a well prepared and
converged calculations. So, I would be so thankful if one could comment on
this.

By the way, this is what I have in my dos.log file.
----------------------------
System = "A3B crystal Solid"
Nmol = 43904
Natom = 43904
dt = 0.2 ps
tmass = 2.05132e+06 amu
V = 415.228 nm^3
rho = 8203.43 g/l
T = 298.15 K
beta = 0.403395 mol/kJ

DoS parameters
Delta = 3.49303e-05
fluidicity = 0.00202656
hard sphere packing fraction = 441.911
hard sphere compressibility = 1.00454
ideal gas entropy = 0.0717008
hard sphere entropy = -0.762789
sigma_HS = 1.99851 nm
DoS0 = 2.3222
Dos2 = 627309
DoSTot = 6.19421
Diffusion coefficient from VACF 0.000169117 10^-5 cm^2/s
Diffusion coefficient from DoS 0.00023386 10^-5 cm^2/s
Heat capacity 0.000623269 J/mol K
------------------------------------------

Best regards,
Alex



On Thu, Feb 4, 2016 at 8:45 AM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 03/02/16 23:52, Alexander Alexander wrote:
>
>> Dear Gromacs user,
>>
>> Normally there is a "*ref-t" [K]  *in .mdp file as reference temperature
>> in
>> NVT calculation, in addition, yet another Temperature must be indicated in
>> "gmx dos *-T* XXX ..." for example in heat capacity (C_v) calculation with
>> quantum correction. So, I was wondering that which of these two
>> temperatures is the one that the heat capacity (C_v) has been calculated
>> in
>> to be reported later?
>>
> To get the simulation temperature run gmx energy
>
>
>> One more question:
>> In C_v calculation, would you please confirm me that the "gmx dos" would
>> give only the quantum correction for C_v? Not the total C_v including
>> quantum correction.
>> IF so, then, the Total C_v  would be:
>> Total C_v = "gmx energy -nmol -fluct_props" + "gmx dos -T ..."
>>
> Have you checked the output from gxm dos?
> It describes everything in quite some detail.
>
>
>> Thank you so much.
>>
>> Cheers,
>>
>> 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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