[gmx-users] ghbond/- hbn option

Erik Marklund erikm at xray.bmc.uu.se
Tue Jan 2 14:03:33 CET 2007

On Tue, 2007-01-02 at 14:54 +0200, OZGE ENGIN wrote:
> Hi,
> I have a  problem with the -hbn option. I could not understand the output given. It is indicated that there is only one type of hydrogen bond is formed between the donor and acceptor (Only one triplet is given). It means that the same hydrogen bond is formed between the same atoms during the simulation?

In principle, yes. There could be hydrogen bonds with the same d-a pair,
but with different hydrogens. That could be the case only if the -merge
option is set, which it is by default.

>  Özge Engin
> Department of Computational Science and Engineering
> Koc University
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Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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erikm at xray.bmc.uu.se

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