Steven Neumann wrote:
On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@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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--
========================================
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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