[gmx-users] g_hbond, residue selection and boundary conditions

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Oct 2 08:40:11 CEST 2008

Hi Nicolas,

>   1. Does g_hbond takes into account the periodic boundary conditions
>   or should first I center the system on my molecule, then run g_hbond?

Yes (pretty much all tools do).

>   2. When I run g_hbond, it prints the message "No option -sel" the
>   usual welcome message and run normally after that. I don't use any
>   -sel option in the command line. Is it because I'm using g_hbond
>   from gmx 3.3.3 with a trajectory from gmx 3.3.1? I use the following
>   command line:

It's an innocent bug in g_hbond, nothing to do with your command-line or system

>   3. When g_hbond ask for 2 groups, is it the same think to specify
>   group1 then group2 and group2 then group1? (assuming group1 and
>   group2 do not overlap)

Yes. The number of hydrogen bonds between A and B is equal to the
number between B and A.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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