[gmx-users] Hydrogen bonds

[Dr. Seema Mishra]

 Thanks, I will try this option too. But now I would want to look at the particular hydrogen bonds between protein and ligand if these h bonds are present after the simulations. So, please let me know how can I interpret this data that I sent? ---
 

     On Saturday, 4 July 2015 11:49 AM, soumadwip ghosh <soumadwipghosh at gmail.com> wrote:
   

 Hi,
  the -hbn option in g_hbond in connection to your issue of determining
the hydrogen bond lifetime or stability does not tell you much. What you
should be looking at is running the g_hbond with -ac flag which gives you
the lifetime and H-bond formation energy between two groups specified by
you in the index file using either a predetermined or the default distance
and angle cut-off. GROMACS  obeys the Luzar and Chandler description of
H-bond kinetics which considers the H-bonds labile and the lifetime of the
same is calculated from the rate constants of H-bond breaking and
re-forming.

Cheers,
Soumadwip
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