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