[gmx-users] Different Cv and Cp

[Faezeh Pousaneh]

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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