[gmx-users] g_hbond

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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