[gmx-developers] Implementation of H-bond analysis

[Anton Feenstra]

Emanuel Peter wrote:
> Dear developers,
> 
> I try to implement the h-bond-analysis tool 'g_hbond or gmx_hbond' into
> mdrun in order to get a dynamic analysis (index list with option -hbn)
> during my MD-run.
> At the moment I don't know how to put this function dump_hbmap into
> mdrun.
> I tried to declare everything in the right way and wrote this function
> below the function write_traj in md.c .
> The compiling produced errors until now and I do not know how to get
> forward.
> I want to make a donor -hydrogen- acceptor list after every nth step in
> the simulation, so I thought it was the best to do this after the
> function write_traj or in write_traj after the function write_trn.

Why do you not read the trajectory (while the mdrun is still running), 
and analyze that with g_hbond?

If you want to do anything specific with the D-H-A list during the run, 
you should probably be thinking about a new interaction function.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Free University  Amsterdam     |
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