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

[Erik Marklund]

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/