[gmx-users] Hydrogen bond with chlorine

Erik Marklund erik.marklund at chem.ox.ac.uk
Mon Feb 10 10:55:16 CET 2014

Others have asked for this functionality before and it would make sense to implement it. However, no one is working on that at the moment and I suspect no one will on the short term since the analysis framework will be overhauled eventually. For now, you can use g_hbond -contact, which allows for atoms other than [ON] to be taken into account, but will omit the angular criterion entirely.


Erik Marklund, PhD
Postdoctoral Research Associate

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road

On 10 Feb 2014, at 09:15, Dhawal Shah <dhawal at squ.edu.om> wrote:

> HI there,
> I have been working on simulations of Urea and Chloride based compounds. In order to analyze my results, I am trying to find hydrogen bond between urea and chlorine. 
> However, I believe, g_hbond only account for O and N atom type hydrogen bonds. 
> How can I find number of hydrogen bonds, if it includes chlorine atoms?
> Best Regards,
> Dhawal 
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