I got a fairly good number using fluctuations formula: cv=3.91J/K.g. I can't seem to figure out what am I doing wrong with g_energy. If someone could run /tutor/water/spc216 and get Cv it would be greatly appreciated.
BTW, I do get interesting numbers for that system when I run g_energy -nmol 216 -ndf 9; Cv=55J/mol.K (close) g_energy -nmol 216 -ndf 10; Cv=88J/mol.K (even closer) Not that I can justify those ndf values though. F. On 9/12/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > Frankie Montenegro wrote: > > Correction: the number is -706.4J/mol.K (negative) . Are you sure 6 is > > correct for ndf? I am running ffgmx force field and all bonds > > constrained spc water. > constrained SPC water has 6 dof (3x3 - 3 constraints). > > Is the temperature constant? > > Maybe you do not need the -nmol flag, otherwise it is time to check the > g_energy source code maybe. > > > F. > > > > > > On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote: > >> David, > >> I didn't realize what the nmol option does, thanks for the tip. But > >> the number went from 12.5 to 706.4 (I'm hiting my forehead on my desk > >> as I type this). BTW why ndf 6 and not 3? For rotation? > >> > >> On 9/12/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > >>> Frankie Montenegro wrote: > >>>> OK but I thought your number comes from equipartition theorem, not > >>>> fluctuations. I think I remember correctly someone posting the code on > >>>> the list a while ago. > >>>> > >>>> Besides, I am also running 3000 SPC waters with Nose-Hoover. After > >>>> 250ps, the number is identical to the one from the example: 12.5 > >>>> J/mol.K > >>> did you use > >>> g_energy -nmol 3000 -ndf 6 ? > >>> > >>>> F. > >>>> > >>>> On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote: > >>>>> I am not sure what I'm missing here. I just ran an example from > >>>>> /tutor/water and got even worse > >>>>> number for specific heat, around 12.5 J/mol.K. Sure, it was with > >>>>> Berendsen T-coupling, no shifted VdW, but one would still expect > >>>>> better number. Anyone? > >>>>> Thanks, Frankie > >>>>> > >>>> _______________________________________________ > >>>> 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 > >>> > >>> -- > >>> David van der Spoel, Ph.D. > >>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > >>> [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > >>> _______________________________________________ > >>> 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 > >>> > > _______________________________________________ > > 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 > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > 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 > _______________________________________________ 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