Dear users, I calculated diffusion constant of a substance using g_msd tool. I also want to calculate thermal conductivity its. By the way,I did npt simulation.
Diffusion constant=alpha Thermal conductivity=k specific heat=Cp density=d alpha=k/(d.Cp) and k=alpha.d.Cp I need d and Cp to calculate k. 1.) To calculate Cp: Prof. Spoel:From http://www.mail-archive.com/gmx-users@gromacs.org/msg37580.html cP = (<H^2> - <H>^2)/kB T^2 (NPT sim) The .edr file gives average enthalpy <H>. According to above formula, I need both H and <H>. How can I get H (not average)? 2.) .edr file: 1 LJ-(SR) 2 LJ-(LR) 3 Coulomb-(SR) 4 Coul.-recip. 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 9 Pressure 10 Box-X 11 Box-Y 12 Box-Z 13 Volume 14 Density 15 pV 16 Enthalpy 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 Mu-X 37 Mu-Y 38 Mu-Z 39 T-System 40 Lamb-System Firstly I calculated Entalphy (16) Afterward I calculated both Etot (7) and pV (15) Enthalpy=Etot+pV Unfortunately, I get "Enthalpy isnt equals to Etot+pV". Why? -- Ahmet Yıldırım -- 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