[gmx-users] hbond correspondence between hbond.log and hbmap.xpm

Justin Lemkul jalemkul at vt.edu
Wed Jun 25 23:40:43 CEST 2014

On 6/25/14, 4:04 PM, Zheng Ruan wrote:
> Hi,
> I'm new to gromacs and right now I'm trying to use g_hbond to analyze
> my trajectory. Basically, I create two selections in .ndx file and try
> to find hydrogen bonds between them. In the output, there is a
> "y-axis" record in hbond.xpm matrix file. The number of the elements
> of "y-axis" is the same with those in hbond.log file. I was wondering
> if they referred to the same thing. That is, if the first row below
> "y-axis" in hbmap.xpm telling me the hbond interaction of the first
> interaction in hbond.log file? Or it's the reverse? I'm asking the
> question because the hydrogen bond reported by g_hbond doesn't seems
> to be consistent with those found by pymol.

The "first" line after the y-axis entry is actually the "last" hydrogen bond 
listed in hbond.ndx (and maybe the .log file; I've never used that one).  The 
listed H-bonds are read from top-down (in order of increasing atom number) while 
the matrix should be interpreted as "bottom-up" to correspond to an increasing 



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