[gmx-users] g_hbond account dieletric medium ?

raja raja_28 at fastmail.us
Thu Aug 3 17:16:36 CEST 2006

Thanks spoel,
The g_hbond merely report formation of hydrogen bonds because of two
electronegative atoms come closure to certain distance and angle. The
force field used to simulate is also not capable of modeling hydrogen
bond (Afraid whether I am right). If the h_bond computes the hydrogen
bonds inside the active site there is certainty is there since
dielectric is low inside but in outside will it be right to compute the
hydrogen bonds mere based on distance and angle between the two
electronegative atoms present in bulk solvent. There could be mere
electrostatic interaction. But how we can prove that proton is shared
between those atoms. 

Sorry if I am making any mistake at fundamental level.

With thanks!

On Thu, 03 Aug 2006 16:12:41 +0200, "David van der Spoel"
<spoel at xray.bmc.uu.se> said:
> raja wrote:
> > Hi XAvier,
> > Thanks again, I meant the resistance caused due to dielectric of water
> > separating two charged residues. I doubt whether it will allow the
> > transfer of charge between them in order for hydrogen bond to be
> > effected.
> It's still unclear.
> The hydrogen bonds you find are there because they are apparently 
> stronger than hbonds with water. However they will still be broken 
> intermittently.
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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