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

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Sun, Sep 18, 2011 at 5:52 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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>
>         <mailto: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
> 
> Thank you Justin. But I  do not get why it is first minimum of RDF? I 
> thought it has to be first maximum of this function - the highest 
> particle density?
> 

Right, the minimum defines the cutoff at which hydrogen bonding is less likely. 
  So the hydrogen bonds should all be within 0.35 nm, not occurring at 0.35 nm. 
  Apologies for my somewhat confusing reply earlier, my mind was going faster 
than my typing :)  The O-O distance of 0.35 nm represents an upper bound for a 
hydrogen bond to occur, not that this is the most populated distance for 
hydrogen bonding.

-Justin

> 
> 
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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 <http://vt.edu/> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
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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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