[gmx-users] g_hbond question

Daniela S. Mueller D.S.Mueller at rug.nl
Wed Mar 22 06:23:00 CET 2006

hi jonathan, 

the actually occuring hydrogen bonds are listed in the log-file. 


On Tue, 2006-03-21 at 14:56 -0800, Moore, Jonathan (J) wrote:
> I created a hydrogen bond map using g_hbond of version 3.3.  The manual indicates that for the hbmap the "Ordering is identical to that in -hbn index file."  However, in my case, the hbmap file contains 13 hydrogen bond indices, but the hbond.ndx file lists 20 sets of donors and acceptors.  Why the mismatch?  How do I know which hydrogen bonds are represented in the map?
> Thanks,
> Jonathan
> ____________________________
> Jonathan Moore, Ph.D.
> Research and Engineering Sciences - New Products
> Core R&D
> The Dow Chemical Company
> 1702 Building, Office 4E
> Midland, MI 48674  USA
> Phone:  (989) 636-9765 
> Fax: (989) 636-4019
> E Mail: jmoore2 at dow.com


Daniela S. Mueller

biologist (Diplom, German degree)

- Molecular Dynamics Group, UQ -

School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
University of Queensland
Qld 4072, Brisbane

Phone: +61-7-33653732

Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm


- MD group, RuG -

Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Website: http://www.rug.nl/gbb/md

More information about the gromacs.org_gmx-users mailing list