[gmx-users] Different Cv and Cp

Faezeh Pousaneh fpoosaneh at gmail.com
Tue Jun 9 17:26:54 CEST 2015


The latter way, I meant in NPT and NVT simulation respectively. I noted
that Gromacs produces Cv and Cp from the latter case.


Best regards


On Tue, Jun 9, 2015 at 5:23 PM, 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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