[gmx-users] Hydrogen bond with chlorine

Jianguo Li ljggmx at yahoo.com.sg
Mon Feb 10 16:05:52 CET 2014

Hi Dhawal,

One way you can try is to manually change the name of chloride to oxygen so that the g_hbond code can treat the new atom name as acceptors. Just modify .gro file, .top file and ions.itp file and get a new tpr file. And use the rerun option of mdrun to get a new trajectory.  Then you can calculate the hbond using the new trajectory.


On Monday, 10 February 2014, 17:49, 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,
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