[gmx-developers] Implementation of H-bond analysis

[Emanuel Peter]

Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> Emanuel Peter wrote:
> > 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.
> >
> Maybe you can be a bit more specific on what you want to do.
> There may be stuff in gromacs that you don't know about yet that may
> be
> helpful for your project.
>
>
>
> > Greetings,
> >
> > Emanuel
> >
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
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>
>
> --
> 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
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>


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