I can't diagnose what is wrong in every case; I can just say that statistical mechanics says that both methods for calculating Cv and both methods for calculating Cp should agree within noise.
On Wed, Jun 10, 2015 at 8:54 AM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > 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 <mrshi...@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 <fpoosa...@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 <mrshi...@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 < > fpoosa...@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 < > mrshi...@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 < > > > fpoosa...@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 < > > > > fpoosa...@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 < > > > > > fpoosa...@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 < > > > > mrshi...@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 < > > > > > > fpoosa...@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? 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