[gmx-developers] Qhop-implementation: integration of motion not correct

[hess at sbc.su.se]

Have you looked at the trajectory?
The whole system is not moving in one direction?

And how do you treat your electrostatics?
With extra sites on the molecule the center of geometry
will not be at the same place as in SPC and much further
away from the center of the dipole.

Berk

> I re-based it on spc myself. But the difference between spc and tip3p is
> much smaller than what I observe. D = 15e-5 cm^2/s.
>
> Erik
>
> Gerrit Groenhof skrev 2011-01-19 08.36:
>> But the masses are the same as for normal water: The watermolecule (2
>> protons and one oxygen) is the framework on which the virtuals are
>> constructed (unless something has changed here as well).
>>
>> However, I remember the first water/hydronium hybdrid was based on
>> tip3p, which has a faster diffission. Can this be the source?
>>
>> Gerrit
>>
>>
>> On 18 Jan 2011, at 22:04, hess at sbc.su.se wrote:
>>
>>> Well, all properties that are right don't depend on the masses.
>>> The diffusion does depend on the masses.
>>> That should be a good hint.
>>>
>>> Berk
>>>
>>>> Hi,
>>>>
>>>> I am implementing the Qhop protocaol in gromacs. I use a special
>>>> topology for the water molecules with three extra virtual particles
>>>> representing the hydronium hydrogens. If a molecule is in the water
>>>> state the nonbonded parameters for the virtual particles are turned
>>>> off
>>>> (q=0, LJ-parameters are always zero). Thus, you'd expect them to
>>>> behave
>>>> just like ordinary spc, which has the same parameters for the water
>>>> part
>>>> of the molecule. However, it does not. I compared simulations with my
>>>> special water in bulk phase (all molecules in the water state) and
>>>> simulations with ordinary spc. Energies, pressures and such thigs are
>>>> almost identical between the simulations, but the diffusion
>>>> coefficient
>>>> is roughly tree times higher with my special water than in a box of
>>>> spc.
>>>> Note that there are no extra calls to do_force() or update functions.
>>>> Do
>>>> any of you have any idea of why this happens?
>>>>
>>>> I'm using leap-frog with Nosé-Hoover (or no) for T-coupling and
>>>> Parinello-Rahman for P-coupling.
>>>>
>>>> Sincerely,
>>>>
>>>> --
>>>> -----------------------------------------------
>>>> Erik Marklund, PhD student
>>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>>> Husargatan 3, Box 596,    75124 Uppsala, Sweden
>>>> phone:    +46 18 471 4537        fax: +46 18 511 755
>>>> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
>>>>
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>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
>
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