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.