[gmx-developers] Implementation of H-bond analysis

Ran Friedman r.friedman at bioc.uzh.ch
Thu Feb 12 11:00:09 CET 2009


The easiest option seems to modify gmx_hbond so that you get the D-H-A
index file as frequently as you want it, unless you really need to use
this as an input during your md simulations.

> 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.
> Greetings,
> Emanuel
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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