Dear Prof. Spoel, Firstly, thanks for your reply. I looked at the paper your said. 1.) To calculate the density d in a constant pressure simulation (in npt simulation): d=M/<V> equation (5) M: mass of the system V:volume of the system Doesnt this formula (equation 5) use when Gromacs calculates the density of system?
2.) The classical-that is, without any quantum corrections-heat capacity cP can be obtained from the fluctuations in the enthalpy (from your paper): cP=<H^2>/(kB.T^2) (equation 13) How did you calculate <H^2>? 3.)You said before " http://www.mail-archive.com/gmx-users@gromacs.org/msg37580.html" cP = (<H^2> - <H>^2)/kB T^2 (NPT sim) This formula doesn't equal to equation 13. There isnt <H>^2 term in equation 13. Why? Thanks in advance 2013/4/12 David van der Spoel <sp...@xray.bmc.uu.se> > On 2013-04-11 22:20, Ahmet yıldırım wrote: > >> could anybody help me please? >> > Check > http://pubs.acs.org/doi/abs/**10.1021/ct200731v<http://pubs.acs.org/doi/abs/10.1021/ct200731v> > > >> >> 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<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 >>> >>> >> >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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