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

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 18 22:11:20 CET 2011

On 2011-01-18 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.
The density is correct too according to g_energy (972 g/l).
Maybe something in update?
> 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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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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