Re: [AMBER] Number of water hits and density

From: Thomas Cheatham <>
Date: Thu, 23 Oct 2014 11:19:06 -0600 (Mountain Daylight Time)

> In a classic paper by T. Chaetham III and P. Kollman "Molecular Dynamics
> Simulations Highlight the Structural Differences among DNA : DNA , RNA :
> RNA , and DNA : RNA Hybrid Duplexes" JACS 1997, they mentioned:
> "For 1000 frames, the expected number of waters per grid element, assuming
> bulk water density, is 4.18. " 1000 Frames corresond to 1 ns in their
> calculations, as the interval was 1 ps.
> Could somebody explain the physical chemistry principles that connects
> number of hits in 1 ns to density. I need exact physical mathematical
> derivation. you can simply to refer to a reference if it is easier. Many
> thanks.

I guess that dates me a bit being referred to as "classic", however I
appreciate the shout out. That paper does have a minor problem with the
units, as it is effectively 4.18 hits per (0.5 A)**3 (i.e. per 0.5A * 0.5A
* 0.5A grid element) not 0.5 A**3 as is listed in the paper...

To figure this out for yourself, convert units of density (g/mL) to
molecules per volume element. Water density is ~1 g/mL. Doing the
conversion is a good learning experience... --tec3

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Received on Thu Oct 23 2014 - 10:30:03 PDT
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