[gmx-users] RDF - first minimum of O-O

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     On 19/09/2011 2:02 AM, Steven Neumann wrote:
> 
>         Hi Gromacs Users,
>         Can anyone explain me why in g_bond the distance is takes <= 3.5nm.
> 
> 
>     If you mean g_hbond, and are using units incorrectly, 0.35nm would
>     be a characteristic distance cut-off for deciding whether a hydrogen
>     bond might exist....
> 
>     That is what I already know...
> 
>  
> 
> 
>         It is said that it comes from the first minimum o RDF of Oxygen
>         atoms in SPC water model. I am sorry, but I just do not catch
>         this. Thank you in advance.
> 
> 
>     Said where? About what? :)
> 
>     Mark
> 
>  
> About cutoff 0.35 nm. See Manual 4.5.4 - page 213 and Figure 8.3 - RDF 
> of O-O atoms in SPC water model. Can you explain this 0.35 nm value as a 
> first minima?

It's there in Figure 8.3, a shallow minimum at 0.35 nm.  For this to occur, then 
ideally the water molecules are forming H-bonds (O-H...O) with an O-O distance 
of 0.35 nm.  Moreover (and I know I posted this to the list before, so it's in 
the archive in greater detail somewhere), the geometric criteria used by g_hbond 
are generally accepted as indicative of hydrogen bonding from crystallographic 
studies.

-Justin

> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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