[gmx-users] g_hbond - which atoms?

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 5 11:53:22 CEST 2004

On Tue, 2004-10-05 at 11:41, Anton Feenstra wrote:
> David van der Spoel wrote:
> > On Tue, 2004-09-21 at 12:20, Samantha Kaye wrote:
> > 
> >>How do I get g_hbond (or something else if I'm using the wrong program)
> >>to tell me which atoms are forming each h-bond? Is that possible?
> > 
> > Yes, you can print out an index file with flag -hbn
> The order of the list in the index file, corresponds to the ordering in
> the other output as well (e.g., the '-hbm' .xpm contact map). Actually,
> the amount and complexity of (dynamic) data on H-bonds is staggering,
> and if there are any suggestions on how to improve the output of g_hbond,
> I'd be happy to here them!

Just let me add that part of g_hbond is broken, due to me implementing
lots of new stuff. The index file stuff should still work, but in
particular the insertion analysis is non-existent for the moment.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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