[gmx-developers] Implementation of H-bond analysis

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 12 11:00:44 CET 2009

> Dear developers,
> At this first step of my project I want to change gromacs in that way to
> do a h_bond-analysis every nth step.
> I wish to get an Donor-hydrogen-acceptor index file from my current
> structure of my simulated protein after for example every 10th step.
> After this change in mdrun.h, md.c or stat.c I would like to have 10
> D-H-A index files after 100 md steps.
> I need this kind of output for further implementations after this
> frequent h-bond-analyses.
> The h-bond tool produces with input -hbn the same D-H-A index list, but
> externally.

Yes, but then waht will you do with it? Some of this functionality is 
already under development in other pieces of code. If you just wish to 
output HBonds, it would be quite straightforward.

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-developers mailing list