[gmx-users] Different Cv and Cp

[Faezeh Pousaneh]

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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>