[gmx-users] How to find Hbonding partner

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 19 19:07:57 CET 2012

Sanku M wrote:
> Hi,
>    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 ?

Use the output of g_hbond -hbn -hbm.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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