[gmx-users] g_hbond simple question

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 23 01:31:11 CEST 2011

Yao Yao wrote:
> Hi Guys,
> I am using g_hbond to analyze hbond between two groups. The manual says 
> "All hydrogen bonds between the two groups are analyzed."
> Does that mean even those hbonds do not hbond to neither of the two 
> groups are still under consideration?

If it doesn't form a hydrogen bond, then it's not a hydrogen bond.  A hydrogen 
bond is defined by the criteria described in the manual.  If those criteria are 
not satisfied, the group does not form a hydrogen bond with whatever other group 
is examined at that time.



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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