[gmx-users] g_hbond

Justin Lemkul jalemkul at vt.edu
Sat Sep 12 03:27:14 CEST 2015

On 9/11/15 2:43 AM, Shahid Nayeem wrote:
> Dear all
> I have used g_hbond with -hbn -hbm flag to get .ndx file and .xpm file.
> Then with xpm2ps I converted .xpm to .eps file. I get half the number of
> rows in .eps file as compared to .ndx file. when using Justins perl script
> I got summary of existence file and here 12 bonds are shown but in .eps
> file only 6 rows are plotted. I know that the bonds are plotted in reverse
> order but here only half number of bonds are plotted in .eps file. please
> help to resolve this issue.

You're probably looking at the wrong entry in the index file.  Hard to imagine 
these could be mismatched.



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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