[gmx-users] Different Cv and Cp

Faezeh Pousaneh fpoosaneh at gmail.com
Tue Jun 9 17:43:42 CEST 2015 

Thank you so much for the reply.

Yes, I use contact applied pressure and I am careful about units. I checked
and average enthalpy and U are close, meaning that PV is negligible. But
the point is variance of enthalpy in NPT differs from variance of energy in
NVT and that causes the difference.

You had given me an article showing that for example for Benzene the
difference in Cv and Cp is 25%, and here Ii get similar ( my molecule is
also carbon ring). But still I can answer why two both ways does not give
same Cv-Cp.
I will follow your suggestion.



Best regards


On Tue, Jun 9, 2015 at 5:29 PM, Michael Shirts <mrshirts at gmail.com> 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).
>
> 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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