Re: water box,

From: David A. Case <>
Date: Wed 18 Dec 2002 16:17:31 -0800

On Wed, Dec 18, 2002, Ioana Cozmuta wrote:
> I was wondering how well does water+Shake in amber compare
> the calculated value for the self-diffusion coefficient of water with the
> experimental values and with for example a calculation where SHake is not
> used? How much does the presence of Shake influence for example the
> calculation of diffusion coefficients and solvation energies of ions in
> water? Is there a reference on this?

TIP3P is, by construction, a rigid water model. Its diffusion properties
are not in very good agreement with experiment. See, e.g.

%A P. Mark
%A L. Nilsson
%T Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K
%J J. Phys. Chem. A
%V 105
%P 9954-9960
%D 2001

> However for production using a value of 0.4 ps for the coupling constant
> for a time step in the dynamics of 1fs I think it is not too soft.
> The coupling constant would be in this case 400*time step
> thus, week enough not to alter the system's
> "natural" fluctuations about the desired temperature. At least that's what
> I would expect. But I think you were saying pretty much the same thing.
> Actually is there some good discussion in a paper on this subject, except
> from Berendsen original paper?

%A T. Morishita
%T Fluctuation formulas in molecular-dynamics simulations with the weak
coupling heat bath
%J J. Chem. Phys.
%V 113
%P 2976
%D 2000


David A. Case                     |  e-mail:
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Received on Wed Dec 18 2002 - 16:17:31 PST
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