[gmx-users] Different Cv and Cp

[Faezeh Pousaneh]

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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