[gmx-users] Different Cv and Cp

Thu Jun 11 20:10:45 CEST 2015

On 09/06/15 17:29, Michael Shirts wrote:
> If the simulation are generating configurations with the Boltzmann
> probability distribution, the results should the same up to error.
>
> Cv and Cp should not be exactly the same, though for liquids at room
> temperature, they are pretty close (look up the precise numbers for the
> fluid you are interested in).
This is not correct. cP and cV can easily differ 20-30%. Not many cV 
have been measured but you can compute the difference from other 
fluctuation formulae, see e.g. Caleman et al. J. Chem. Theory Comput. 
2012, 8, 61–74, http://dx.doi.org/10.1021/ct200731v.
Note that to get accurate numbers you need quantum corrections as well. 
My group are working on implementing a method for that in gmx dos.

>
> Are you calculating enthalpy as U + PV, where P is the constant APPLIED
> pressure, not the instantaneous pressure, and PV is in same units?  Since
> the PV term should be quite low for liquids, the two heat capacities should
> be relatively close (within noise -- fluctuation based calculations I think
> are noisier).
>
> Else you need to check if the Boltzmann distributions are being correctly
> generated: See the code and paper describing it linked here:
> https://github.com/shirtsgroup/checkensemble
>
>
>
>
> On Tue, Jun 9, 2015 at 11:23 AM, Faezeh Pousaneh <fpoosaneh at gmail.com>
> wrote:
>
>> Dear Michael,
>>
>> Can I ask a question concerning your previous email,
>> I followed
>>
>> Cv = (d<U>/dT)_V
>>
>> Cp = (d<H>/dT)_P
>>
>> for my lutidine molecule, and I get same values for Cv and Cp. But when I
>> test with
>>
>> kB T^2 c_P = Var (Enthalpy)
>> kB T^2 c_V = Var (Energy)
>>
>> I get 40 J/mol.K difference in Cv and Cp.
>>
>> Mean that fluctuation play big role. Which way of checking I can rely?
>>
>>
>> Best regards
>>
>>
>> On Tue, May 26, 2015 at 3:38 PM, Michael Shirts <mrshirts at gmail.com>
>> wrote:
>>
>>> By definition (more fundamental that fluctuation formulas)
>>>
>>> Cv = (d<U>/dT)_V
>>>
>>> Cp = (d<H>/dT)_P
>>>
>>> Run two simulations at different T and estimate the derivatives.
>>>
>>> On Tue, May 26, 2015 at 5:12 AM, Faezeh Pousaneh <fpoosaneh at gmail.com>
>>> wrote:
>>>
>>>> Dear Michael,
>>>>
>>>> I still would like to know what was your method you mentioned on last
>>>> paragraph, just for learning:
>>>>
>>>> ''Also, to be sure, you should double check by calculating both heat
>>>> capacities by finite difference formulas as well with two simulations
>> at
>>>> T+dt/2 and T-dt/2 -- if the fluctuation and finite difference resutls
>>> don't
>>>> agree within propagated error, then something is off.''
>>>>
>>>> ?
>>>> thanks
>>>>
>>>>
>>>> Best regards
>>>>
>>>>
>>>> On Mon, May 25, 2015 at 5:10 PM, Faezeh Pousaneh <fpoosaneh at gmail.com>
>>>> wrote:
>>>>
>>>>> Dear Andre,
>>>>>
>>>>> thank you for the link, you are probably right, It seems that my
>>> molecule
>>>>> has the difference Cp-Cv in the same range as benzene (since it has
>>> also
>>>>> ring structure).
>>>>>
>>>>>
>>>>> Best regards
>>>>>
>>>>>
>>>>> On Mon, May 25, 2015 at 4:44 PM, Faezeh Pousaneh <
>> fpoosaneh at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Dear Michael,
>>>>>>
>>>>>> I use  Parrinello-Rahman for barostat and v-rescale for thermostat.
>>>>>>
>>>>>> Sorry, could you explain more the second paragraph please? I did not
>>> get
>>>>>> the method. What I checked so far is checking if gromacs correctly
>>> gives
>>>>>> Cv,Cp= Var(Energy or Enthalpy)/kBT^2 , and I find that it gives.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Best regards
>>>>>>
>>>>>>
>>>>>> On Mon, May 25, 2015 at 4:11 PM, Michael Shirts <mrshirts at gmail.com
>>>
>>>>>> wrote:
>>>>>>
>>>>>>> Are you running with the Berendsen thermostat or barostat?  The
>>> gromacs
>>>>>>> g_energy functions for heat capacity use the fluctuation formula,
>> and
>>>> the
>>>>>>> fluctuations with both of these algorithms are wrong (as should be
>>>>>>> printed
>>>>>>> in the log file warning message). Make sure you use
>>> ensemble-preserving
>>>>>>> thermostats if you want fluctuation properties.
>>>>>>>
>>>>>>> Also, to be sure, you should double check by calculating both heat
>>>>>>> capacities by finite difference formulas as well with two
>> simulations
>>>> at
>>>>>>> T+dt/2 and T-dt/2 -- if the fluctuation and finite difference
>> resutls
>>>>>>> don't
>>>>>>> agree within propagated error, then something is off.
>>>>>>>
>>>>>>>
>>>>>>> On Mon, May 25, 2015 at 5:59 AM, Faezeh Pousaneh <
>>> fpoosaneh at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I do not know why I obtain two difference cp and cv from NVT and
>>> NPT
>>>>>>>> simulations.
>>>>>>>> What I do is, I take 1000 lutidne molecules, and I do firstly an
>>>> energy
>>>>>>>> minimization with steep integrator, then NPT simulation at T=300
>>> and
>>>>>>> P=1
>>>>>>>> atm for 10ns, (I obtain Cp= 230), then I run NVT for 10 ns with
>>> same
>>>>>>> mdp
>>>>>>>> file except no pressure coupling, and with initial .gro file
>>> obtained
>>>>>>> from
>>>>>>>> NPT run, (I obtain Cv=180).
>>>>>>>> Does some one know where is my mistake? (In both runs, I obtain
>> Cv
>>>> and
>>>>>>> Cp
>>>>>>>> from g_energy and in different time intervals and after
>>> equilibrited
>>>>>>> time)
>>>>>>>>
>>>>>>>>
>>>>>>>> Best regards
>>>>>>>> --
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
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