[gmx-users] Hydrogen bonds

soumadwip ghosh soumadwipghosh at gmail.com
Sat Jul 4 08:18:49 CEST 2015

   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


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