[gmx-users] Fwd: C_v and Temperature
alexanderwien2k at gmail.com
Fri Feb 5 11:02:37 CET 2016
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
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
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
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
On Thu, Feb 4, 2016 at 8:45 AM, David van der Spoel <spoel at xray.bmc.uu.se>
> 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
>> 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
>> 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.
> 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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