[gmx-users] Different Cv and Cp

Faezeh Pousaneh fpoosaneh at gmail.com
Wed Jun 10 14:55:33 CEST 2015 

Dear Michael,

Could you please comment on my last question, thanks a lot.
I have noticed that when I run both NVT and NPT simulations from a same
.gro file (obtained from energy minimization) I obtain same Cv and Cp for
two ensembles. However, so far I was running NVT after NPT (meaning I used
.gro file obtained from NPT as initial configuration for NVT, since I
wanted to have correct volume). The second way gives that big difference in
Cv and Cp.
I run a long simulations in all cases, but why both ways produce such
difference?



Best regards


On Tue, Jun 9, 2015 at 5:45 PM, Michael Shirts <mrshirts at gmail.com> wrote:

> The variance formula is derived from the derivative formula + the
> assumption the distribution in Boltzmann, so they must agree if the
> distribution is Boltzmann.
>
> On Tue, Jun 9, 2015 at 11:43 AM, Faezeh Pousaneh <fpoosaneh at gmail.com>
> wrote:
>
> > 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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