[gmx-users] Different Cv and Cp
fpoosaneh at gmail.com
Mon May 25 16:45:38 CEST 2015
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.
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>
> > 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
> > 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
> > Best regards
> > --
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