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

Erik Marklund erikm at xray.bmc.uu.se
Tue Jan 18 22:01:48 CET 2011


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.


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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