[gmx-users] H-Bonding residues against specific frames

Justin Lemkul jalemkul at vt.edu
Mon Feb 9 13:27:44 CET 2015

On 2/8/15 6:08 PM, Agnivo Gosai wrote:
> Dear Users
> I am using g_hbond to get the H-bonds for a particular simulation over the
> entire trajectory. In the log file I can find which reesidues are forming
> H-bonds.
> However , I want the H-bonds formed over the entire simulation length frame
> wise or for a particular frame. How can I do so ?
> I was thinking of extracting every frame (using trjconv) from my total of
> 501 frames and running g_hbond on each of the frames. But that seems to be
> a laborious process. Is there any way out ?

Use -hbm -hbn to write an H-bond existence matrix, and use the index file 
created by -hbn to map out which ones are which.



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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