[gmx-users] Re: g_hbond

Jian Zou zouj01 at mails.tsinghua.edu.cn
Fri Aug 11 06:20:48 CEST 2006

Hi David,

I read your JPCB paper (JPCB-110-4393) and it says that the geometric 
criteria with DA distance and DHA angle is employed. Therefore I'm a little 
confused which angle is indeed used to determine the Hbond, HDA or DHA?


Jian Zou

David van der Spoel wrote:
> Dear David,
>  ok. Now I understand HDA criterion. Can you give me a reference
> where I can find the differences between HDA criteria and OHD criteria
> and why one of them is preferable than the other?

We implemented this in order to reproduce a number of publications. It
is difficult to say that one is to be preferred over the other.  If
something an energy-based criterium could be preferred, however
classical mechanics is not good enough to quantitatively describe the
details of hydrogen bonding anyway. Some interesting refs are:

   author =   {F. W. Starr and J. K. Nielsen and H. Eugene Stanley},
   title =   {Hydrogen-bond dynamics for the extended simple point
charge model of water},
   journal =   {Phys. Rev. E},
   year =   2000,
   volume =  62,
   pages =  {579-587}

   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

   author =   {D. van der Spoel and P. J. van Maaren and P. Larsson and
N. Timneanu},
   title =   {Thermodynamics of hydrogen bonding in hydrophilic and
hydrophobic media},
   journal =      {J. Phys. Chem. B},
   year =         2006,
   volume =       110,
   pages =   {4393-4398}

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