[gmx-users] g_hbond never shows hbond with HW2

Justin Lemkul jalemkul at vt.edu
Fri May 1 17:30:46 CEST 2015

On 5/1/15 11:27 AM, Ebert Maximilian wrote:
> Dear list,
> I discovered something strange today. In my hbond search i find only HW1 of the water forming a hydrogen bond as donor hydrogen and never HW2. Is this due to the fact that I am using SPC water? I can see the atom IDs of HW2 in the [ donors_hydrogens_Water ] entry in the ndx file. So technically GROMACs searched for HW2 donor connections but never finds any. However, thousands of hbonds are found with HW1.
> Any thoughts on that? Thanks,

This is default behavior because of -merge.  If you want to differentiate 
between different H on the same donor, use -nomerge.



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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