[gmx-users] Different Cv and Cp

[Faezeh Pousaneh]

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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>>
>>
>