[gmx-users] Re: g_hbond

[David van der Spoel]

Jian Zou wrote:
> 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?
> 
> 
Oops, that is wrong in the paper! It is HDA in the program.

In the literature, e.g. the two papers by Starr et al. and the paper by 
Xu & Berne it is said that the O-H ... O should be less then thirty 
degrees, which is also what I wrote in my paper (DHA) however that does 
not make sense, because that angle is more than 90 degrees in a HB. 
Sorry about the confusion, but I'm sure that everyone either uses HDA or 
HAD. We can reproduce exactly the numbers of Xu & Berne with g_hbond for 
TIP4P and SPC/E.


> Regards,
> 
> 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:
> 
> @Article{Starr2000a,
>    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}
> }
> 
> @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
> }
> 
> @Article{Spoel2006b,
>    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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-- 
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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