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

[David van der Spoel]

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