Vitaly Chaban wrote: >> I've got a discrepancy calculating the diffusion coefficient via >> Green-Kubo equation and via Einstein equation. >> > > >> $ g_velacc -nonormalize -acflen 1001 >> $ g_analyze -f vac.xvg -integrate >> Do I miss any important keyword here? It seems the result of integration is >> not >> correct in this case. >> > > For the VACF of the molecules: > $ g_velacc -nonormalize -acflen 1001 -mol -n index.ndx (index.ndx > contains the number of molecules for the calculation) > > $ g_analyze -f vac.xvg -integrate > > The result should be finally divided by 3. > > Hello,
why should one use a prefactor of 1.0/3.0 ? I thought the flag -mol calculates the momentum autocorrelation function, so in my opinion the result has to be divided by the square of the masses of the molecules to obtain the diffusion constant. Best Regards, Flo > -- > Vitaly V. Chaban > School of Chemistry > University of Kharkiv > Svobody sq.,4 > Kharkiv 61077, Ukraine > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- Florian Dommert Dipl.-Phys. Computational and Theoretical Softmatter & Biophysics group Frankfurt Institute for Advanced Studies Johann-Wolfgang-Goethe University Ruth-Moufang-Str. 1 60438 Frankfurt am Main Phone: +49(0)69 / 798 - 47522 Fax: +49(0)69 / 798 - 47611 EMail: [EMAIL PROTECTED] Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
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