[gmx-users] Different Cv and Cp

[Michael Shirts]

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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