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
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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
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