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? 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-requ...@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-requ...@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-requ...@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-requ...@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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.