[gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

[Frankie Montenegro]

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 <spoel at xray.bmc.uu.se> 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 <frankie.montenegro at gmail.com> 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 <spoel at xray.bmc.uu.se> 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 <frankie.montenegro at gmail.com> 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
> >>>>>
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> >>> --
> >>> 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.
> >>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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> --
> 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.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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