[gmx-users] g_hbond index

Justin Lemkul jalemkul at vt.edu
Wed Dec 19 17:36:27 CET 2012

On 12/19/12 9:37 AM, Kavyashree M wrote:
> Dear users,
> While using g_hbond, does it make any difference if I give option
> 18 and 1 or 1 and 18?

Order does not matter.

> I wanted to find the hydrogen bonding of a group of residues with
> the whole protein so I had an index of this group. When I give the
> option as 18 (index number) and 1 (whole protein), I get several
> messages
> "Hm. This isn't the first time I found this donor (...,...)"
> But later it does calculates. does this mean that it is double counting
> those interactions?

What is group 18?  Be mindful of the g_hbond requirement that the chosen groups 
must be completely unique or completely overlapping.



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


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