[gmx-users] Re: g_hbond
David van der Spoel
spoel at xray.bmc.uu.se
Fri Aug 11 08:24:54 CEST 2006
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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