[gmx-developers] Implementation of H-bond analysis

[Emanuel Peter]

Quoting Anton Feenstra <feenstra at few.vu.nl>:

> 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
> |
> |(   |   )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands
> |
> | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136
> |
> |             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/
> |
> |             | "You Could Be a Shadow" (The Breeders)
> |
>
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Dear developers,

I need to implement this h_bond-analysis D-H-A into the runprogram.
Someone asked me why not to write it in a kind of a perl script that
connects mdrun with a frequent use of the g_hbond tool.
At this stage I think it would be the best to implement a new
interaction function with parts taken out of the g_hbond analysis tool.
One of the main problems in the source code of Gromacs is that there is
a huge amount of different functions which sometimes are declared
anywhere but not in the headers that I was looking for.

Greetings,

Emanuel