[gmx-users] g_hbond account dieletric medium ?

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 3 17:29:19 CEST 2006

raja wrote:
> 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.
OK, I see what you mean now. First whether or not there is a HBond is a 
matter of taste. One can use a geometric criterion or an energy 
criterion to decide that. In molecular modeling the transfer of a proton 
is not taken into account explicitly. Sharing a proton does not exist in 
reality, in my opinion, however one can have fast shuffling of a proton 
between two sites, e.g. in the active site of HIV protease, where there 
are two Asp residues, one of which is protonated.

The following references may be helpful:
   author =       {F. W. Starr and J. K. Nielsen and H. Eugene Stanley},
   title =        {Hydrogen-bond dynamics for the extended simple point 
charge mo
del of water},
   journal =      {Phys. Rev. E},
   year =         2000,
   volume =       62,
   pages =        {579-587}
   author =       {D. van der Spoel and P. J. van Maaren and P. Larsson 
and N. Ti
   title =        {Thermodynamics of hydrogen bonding in hydrophilic and
hydrophobic media},
   journal =      {J. Phys. Chem. B},
   year =         2006,
   volume =       110,
   pages =        {4393-4398}
   author =       {K. Modig and B. G. Pfrommer and B. Halle},
   title =        {Temperature-dependent hydrogen bond geometry in 
liquid water},
   journal =      {Phys. Rev. Lett.},
   year =         2003,
   volume =       90,
   pages =        075502

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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