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

[Steven Neumann]

On Sun, Sep 18, 2011 at 5:52 PM, Justin A. Lemkul <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>>> 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?

>
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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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