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

Erik Marklund erikm at xray.bmc.uu.se
Wed Jan 26 19:41:25 CET 2011

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/

More information about the gromacs.org_gmx-developers mailing list