Re: [gmx-users] Different Cv and Cp

Just for those who may face with similar problem as I had. I found where my mistake was. The problem: I have been obtaining Cv and Cp differently for Lutidine. The obtained heat capacities in Groamcs were consistent with kB T^2 c_P = Var (Enthalpy) kB T^2 c_V = Var (Energy) but not with Cv =

Re: [gmx-users] Different Cv and Cp

Dear Andre, Many thanks for the message, was very useful. I followed your comments carefully. Below; (1) I would suggest you not to take the last frame of the NPT simulation as the correct volume. You should instead take an average volume from the equilibrated NPT simulation and then edit

Re: [gmx-users] Different Cv and Cp

On 09/06/15 17:29, Michael Shirts 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

Re: [gmx-users] Different Cv and Cp

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

Re: [gmx-users] Different Cv and Cp

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

Re: [gmx-users] Different Cv and Cp

Dear Faezeh, Michael is absolutely right, both methods should yield exactly the same Cp and Cv values, but that is only true in the limit of infinite sampling. If sampling is not infinite but is long enough, Cp and Cv values should agree within the statistical uncertainty of each method. So it

Re: [gmx-users] Different Cv and Cp

Dear Michael, Can I ask a question concerning your previous email, I followed Cv = (dU/dT)_V Cp = (dH/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.

Re: [gmx-users] Different Cv and Cp

The latter way, I meant in NPT and NVT simulation respectively. I noted that Gromacs produces Cv and Cp from the latter case. Best regards On Tue, Jun 9, 2015 at 5:23 PM, Faezeh Pousaneh fpoosa...@gmail.com wrote: Dear Michael, Can I ask a question concerning your previous email, I

Re: [gmx-users] Different Cv and Cp

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.

Re: [gmx-users] Different Cv and Cp

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

Re: [gmx-users] Different Cv and Cp

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

Re: [gmx-users] Different Cv and Cp

By definition (more fundamental that fluctuation formulas) Cv = (dU/dT)_V Cp = (dH/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

[gmx-users] Different Cv and Cp

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

[gmx-users] different Cv and Cp in liquid phase

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

Re: [gmx-users] Different Cv and Cp

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

Re: [gmx-users] Different Cv and Cp

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

Re: [gmx-users] Different Cv and Cp

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.