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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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