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

[Erik Marklund]

I'm simulatimg with cut-offs to keep things simple.

I tried calculating the diffusion coefficient with g_msd -rmcomm too, 
but that didn't make much of a difference.

It's true that thw center of geometry is shifted away from the dipole 
center, but I don't see how this would affect the simulations other than 
that the "effective" cut-off would be increased slightly. The extra 
particles have q=0 and invmass=0. I don't expect them to be subject to 
any force under these conditions, thus not propagating any force to the 
water atoms. Or am I wrong?

Thanks for helping out,

Erik

hess at sbc.su.se skrev 2011-01-19 09.15:
> 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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-- 
-----------------------------------------------
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/