[gmx-users] How to find Hbonding partner

Sanku M msanku65 at yahoo.com
Thu Jan 19 18:20:48 CET 2012

   I am wondering whether there is any way in GROMACS that one can find which groups are the main Hbonding partners in a trajectory. For example, if I simulate a peptide in water, I want to know during the simulation, which particular atoms in the peptides are making most of the Hbonds with water as a function of time. I find g_hbond can tell us the total number of Hbond between two groups as a function of time but, can it specify which groups are making the Hbonds most of the time ?

Any help will be appreciated.

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