[gmx-users] g_hbond, residue selection and boundary conditions
tsjerkw at gmail.com
Thu Oct 2 08:40:11 CEST 2008
> 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
3584 CH Utrecht
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