jalemkul at vt.edu
Fri Sep 28 16:29:51 CEST 2012
On 9/28/12 8:53 AM, Gavin Melaugh wrote:
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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