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

Steven Neumann s.neumann08 at gmail.com
Sun Sep 18 22:34:11 CEST 2011


On Sun, Sep 18, 2011 at 7:25 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<Mark.Abraham at anu.edu.au>
>> >
>>        <mailto:Mark.Abraham at anu.edu._**_au
>>        <mailto:Mark.Abraham at anu.edu.**au <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
>

Thank you Justin, that helped a lot! Easy explanations makes life very
simple! :)

>
>
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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://vt.edu/Pages/Personal/justin>
>>    <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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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