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

[Frankie Montenegro]

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.
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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