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

[Erik Marklund]

Erik Marklund skrev 2011-01-18 22.01:
> 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,
>
Just thought I'd say I have this down now. It was entirely unrelated to 
the mdp options. One of those pesky indexing errors we've all learned to 
hate as programmers.

Thanks for all the input.

-- 
-----------------------------------------------
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/