[gmx-developers] Implementation of H-bond analysis
feenstra at few.vu.nl
Wed Feb 11 19:55:47 CET 2009
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
> 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
> 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.
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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam |
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| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
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