[gmx-users] shell water and epsilon
David L. Bostick
dbostick at physics.unc.edu
Fri May 13 19:18:55 CEST 2005
Thanks for the itp file. Should I be running the shell models with double
precision mdrun? At least that's what I gather from looking at previous
postings to the list. Can one get by with single precision?
Sorry to be unclear about my question. I suppose in comparing your paper's
figure 5 to Lamoureux's figure 2, it seems that somehow, Lamoureaux's
epsilon appears to converge after 500 ps, and the SW epsilon is still
changing after 1500 ps. I meant to ask why there is this difference, even
if you had to speculate. Also, the dielectic constant for SW, is high (or
appears to be high), and
in your paper, it was mentioned that it was possibly due to LJ interactions
not making the water "sticky" enough ... connecting the diffusion
coefficient with the high epsilon. Has there been any exploration to change
the SW parameters a bit?
Is it really possible to run the Lamoureux model in the same way as was
published? Is it possible to have a Nose-Hoover heat bath on the
oxygen-Drude pair's relative motion in the water's local reference frame?
This heat bath is to be uncoupled from the global heat bath on the
hydrogens and the center of mass of the drude pair. Their argument was that
if the oxygen-Drude pair's heat bath was held at 1 K, the model stays close
to the self-consistent-field regime.
> I don't understand the question I'm afraid...
> Do you mean Fig. 2?
> One thing that is different from our SW models is that they do not
> minimize the shell positions at each time step, but rather give it a
> mass of 0.4 amu. With a timestep of 1 fs it seems that the shells will
> not be very well optimized, i.e. the model violates the Born-Oppenheimer
> I'm attaching the itp file, with a real shell that is minimized at each
> time step. If you want to reproduce the original work you can change the
> particle type to A and give it a small mass.
> You will need yesterdays CVS code to run it...
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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