[gmx-users] g_hbond

Justin Lemkul jalemkul at vt.edu
Tue Aug 4 17:25:35 CEST 2015

On 8/4/15 9:40 AM, jwillcox at andrew.cmu.edu wrote:
> Hello,
> I'm trying to use g_hbond to calculate H-bonds between two different
> species, but it seems to be counting the donor atom as an acceptor as
> well.
> e.g. instead of measuring the H-bonds of water to acetate oxygens, it
> seems to be measuring the H-bonds of water to acetate oxygens and water
> oxygens
> Is there a way to specify that I only want to look at the water-acetate
> H-bonds and not water-water H-bonds?

Proper use of index groups will solve this.  You unfortunately haven't provided 
us with any relevant details about how you're doing the calculation, so no one 
can really comment further.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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