Dear all, I am trying to calculate Cv of a pure alkane 125 molecules with actual density, and here is what I have done:
1- Cv: Run NVT > g_energy>select T and Etot=total energy As I issue g_energy *.edr Heat Capacity Cv: 12.4787 J/mol K (factor = 0.000369503) And when I choose –nmol XXX Heat Capacity Cv: 13.4007 J/mol K (factor = 0.0462137) - Do I have to use –nmol? What would be the unit with –nmol ? and as I issue g_energy using 4.5.3 Temperature dependent fluctuation properties at T = 299.987. #constr/mol = 0 Heat capacity at constant volume Cv: 341.734 J/mol K and with -nconstr # of bonds Temperature dependent fluctuation properties at T = 299.987. #constr/mol = 19 Heat capacity at constant volume Cv: 262.746 J/mol K - From this I am guessing what 4.0.7 reports is not correct!? but still what I am getting from 4.5.3 is far from actual reported value (around 170). I guess I am missing something..! or Is the difference acceptable? g_energy says: you will need to give the number of constraints per molecule –nconstr - so I need to count how many bonds are fixed in the molecule as I am setting constraints= all-bonds? The way to this is counting no. of bonds? What about macromolecules? Is there an easier way of finding number of constraints? 2- Cp: I did NPT, g_energy *.edr -nmol XXX -nconstr (4.5.3) I want to select T and enthalpy but since enthalpy is not on the list I select total-energy (which is Etot I think) and pv terms but g_energy is still giving Cv! Property Energy terms needed --------------------------------------------------- Heat capacity Cp (NPT sims): Enthalpy, Temp Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Total Energy 86.1571 0.085 1.55565 -0.0944531 (kJ/mol) Temperature 300.074 0.07 5.77219 0.318146 (kJ/mol) pV 15.8128 0.061 1080.82 -0.249203 (kJ/mol) Temperature dependent fluctuation properties at T = 300.074. #constr/mol = 19 Heat capacity at constant volume Cv: 325.067 J/mol K Can you please guide me where the problem lies? ------------------------------------------------------- again Cv : to compare with constraints=none but still -nconstr should be on otherwise I values are more off. Total Energy 132.418 0.051 1.77314 0.144794 (kJ/mol) Temperature 300.008 0.052 4.50209 0.15866 (kJ/mol) Temperature dependent fluctuation properties at T = 300.008. #constr/mol = 20 Heat capacity at constant volume Cv: 442.016 J/mol K 3- Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp Isothermal compressibility: Vol, Temp Adiabatic bulk modulus: Vol, Temp Since volume appears for calculation of the above properties , does this imply only NPT results in these properties? and wanted to make sure what 4.5.3 reports is reliable.. Many thanks for you time! Best,
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists