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

hess at sbc.su.se hess at sbc.su.se
Tue Jan 18 22:04:46 CET 2011

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.


> 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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