[gmx-users] g_hbond

Justin Lemkul jalemkul at vt.edu
Fri Sep 28 16:29:51 CEST 2012

On 9/28/12 8:53 AM, Gavin Melaugh wrote:
> Hi
> I have an alcohol system and I want to calculate the number of H bonds
> during the trajectory.
> My atom type labels are C2-C2-C2-CO-OH-HO.  CO denotes carbon bonded to
> oxygen, OH denotes alcohol oxygen, and HO denotes alcohol hydrogen.
> In g_hbond how do I specify my groups to consider for H bonding. If I
> uses group 0 which is the whole system it says that I have twice as many
> acceptors as donors, which shouldn't be the case.

g_hbond uses atom names (not types) to determine what is considered a donor, 
acceptor, or H atom.  If there is a problem with the number of acceptors or 
donors, then there is a problem with the way the atoms are named.  Without 
seeing the [atoms] section of the topology or relevant snippet of the coordinate 
file, it's hard to say what's going on at this point.



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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