could anybody help me please?
2013/4/11 Ahmet yıldırım <ahmedo...@gmail.com> > 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 > -- 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
