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

[Erik Marklund]

I will try another electrostatic setup then. Thanks.

Erik

hess at sbc.su.se skrev 2011-01-19 09.51:
> Really plain cut-off's???
> That itself is already a sin for polar systems such as water.
> But since such a setup doesn't use properly buffered cut-off's,
> you'll get nasty artifacts, especially if the center of geometry
> of the charge groups is far off from the center of the dipole.
>
> I actually don't see what is simpler about using plain cut-off's.
> Changing cut-off to PME is all you would need to do.
> But even then there might still be some buffering issue.
> Using pme-switch with a larger buffer would solve this.
> But reaction-field-zero with a large buffer would also do.
>
> These issues are the reason why I would like to have buffered
> cut-off by default in Gromacs, but unfortunately that will cost
> us some performance. I'm working on that though.
>
> Berk
>
>> 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/
>>
>> --
>> gmx-developers mailing list
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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/