[gmx-users] g_hbond index

Justin Lemkul jalemkul at vt.edu
Wed Dec 19 18:22:53 CET 2012

On 12/19/12 11:43 AM, Kavyashree M wrote:
> Sir,
> I thought that the order should not matter but when I used 18 - 1
> and 1 - 18 the graph were slightly off.
> Group 18 is a set of residues in that protein with some unique property.
> I wanted to see the variation of Hbond of these residues with the whole
> protein. so group 18 is a subset of group 1.

You see a difference likely because you are invoking the command incorrectly 
(with overlapping index groups) and it is affecting the way the donor and 
acceptor arrays are constructed.  The proper method of analysis is to monitor 
H-bonds within "group 18" and then between "group 18" and whatever part of the 
protein that does not overlap with it.



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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