[gmx-users] question about g_hbond

Justin Lemkul jalemkul at vt.edu
Sun Sep 1 18:53:19 CEST 2013

On 9/1/13 12:50 PM, Nidhi Katyal wrote:
> Hello,
> I would like to calculate number of contacts between two groups, for which
> I am using following command:
> g_hbond -f *.xtc -s *.tpr -num *.xvg -contact -b 49000 -e 50000
> I am getting 0 as the output. But when I am calculating number of hydrogen
> bonds between the same two groups by using the above command without
> contact option I  am getting 5.2 as the output.
> My question is wouldn't number of contacts be higher than number of
> hydrogen bonds since hydrogen bonds are subset of contacts.

In theory, but something might be failing.  What are the groups you are 
choosing?  What is your expected outcome?  What does the output of g_mindist -on 
give you?



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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