[gmx-developers] Implementation of H-bond analysis

[David van der Spoel]

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
> 
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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