[gmx-users] g_hbond account dieletric medium ?

[raja]

Dear Spoel,
Thank for your elaborate answer and references. Some times this forum
serves more than just for gromacs, yes it helps to understand some
basics understanding of physical chemistry. I learned lot of fundamental
concepts of protein modeling in this forum, which I could never
understand by reading a book or journal.

Regards,
B.Nataraj
in 
On Thu, 03 Aug 2006 17:29:19 +0200, "David van der Spoel"
<spoel at xray.bmc.uu.se> said:
> 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:
> @Article{Starr2000a,
>    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}
> }
> @Article{Spoel2006b,
>    author =       {D. van der Spoel and P. J. van Maaren and P. Larsson 
> and N. Ti
> mneanu},
>    title =        {Thermodynamics of hydrogen bonding in hydrophilic and
> hydrophobic media},
>    journal =      {J. Phys. Chem. B},
>    year =         2006,
>    volume =       110,
>    pages =        {4393-4398}
> }
> @Article{Modig2003a,
>    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.
> ________________________________________________________________________
> 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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-- 
  raja
  raja_28 at fastmail.us

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