Re: Guideline for selecting water box size.

From: Aron Broom (
Date: Sun Feb 16 2014 - 19:12:30 CST

As a minimum you may want the distance from the surface of the protein to
be 1/2 the long-range cutoff. That way, a protein atom on one side of the
protein does not explicitly "see" a protein atom on the other side, and so
the only inter-protein interactions are of a bulk nature through PME.
Beyond that it's probably largely trail and error (at least I've not heard
of anything more concrete), although one does see a lot of using the full

Keep in mind that while even a box 20A from the surface will give a protein
concentration far in excess of anything physiological, you won't have the
problems a physiological system would have at that concentration (namely
aggregation) because you just have one molecule.

One additional consideration may be if you have molecules in solution other
than water, such as salts or some organic. In that case, you probably want
the volume to be large enough that you can include a enough of these other
molecules to be meaningful (i.e. if you want to have 150mM NaCl, you
probably want on the order of at least 10 ions or more in order to avoid
problems with small numbers).

I would say go as small as you can get away with. If going with 1/2 the
cutoff doesn't seem to behave differently than say the full cutoff, why
waste computational time?

On Sun, Feb 16, 2014 at 7:49 PM, Hyuntae Na <> wrote:

> Dear All,
> Is there any guideline for selecting the water box size for variant size
> of proteins, dna, and so on?
> Some might say that 10A from the surface of a protein is enough, and 20A
> is too costly. However, it is not clear how the water box size is decided.
> Does the box size depend on the electrostatic cutoff distance (assuming it
> is 12A)? Is its selection from an experience or from a rationale? I just
> begin to wonder how it is decided.
> Thank you all.
> Best regards,
> -- Hyuntae

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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