Re: [AMBER] Number of water hits and density

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Thu, 23 Oct 2014 13:18:00 -0400

Tom would know best, but if I were to do this I would take the known
concentration of water (approx 55 mol/L, but calculate it exactly for your
water model), and use the volume of the grid cell to get the number of
waters per cell. then you can multiple by the number of frames to get
expected count over the whole run.

On Thu, Oct 23, 2014 at 11:01 AM, Suhaib Shekfeh <s.shekfeh.gmail.com>
wrote:

> 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.
>
>
> --
> Pharmacist. Suhaib Shekfeh
> Medicinal Chemistry
> Institute of Pharmacy
> Martin-Luther-Universit├Ąt Halle-Wittenberg
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>
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Received on Thu Oct 23 2014 - 10:30:03 PDT
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