[gmx-developers] g_hbond h-bond-analysis

[Erik Marklund]

Emanuel Peter skrev:
> Quoting Anton Feenstra <feenstra at few.vu.nl>:
>
>   
>> Emanuel Peter wrote:
>>     
>>> Dear developers,
>>>
>>> Could you tell me some more about the g_hbond tool with its -hbn
>>> index-file-option?
>>>
>>> Does this function dump-hbmap write down all h-bonds of the
>>>       
>> selected
>>     
>>> group that have existed over the whole trajectory or does it take
>>>       
>> just
>>     
>>> the last written trn-frame?
>>>       
>> The hbmap will hold a matrix of <number of hbonds> x <number of
>> frames>,
>> and stores the existance of each hbond (from your -hbn index file)
>> for
>> each frame in your trajectory.
>>
>> Dear developers,
>>     
>
> Does the tool g_hbond with its option -hbn then show a list of all
> stored hbonds per frame or does it just show a list of hbonds that
> existed in the last frame?
>   
All hbonds in the matrix, which are all hbonds there ever was. What's 
even better: the two files match so that you can tell which D(H)A each 
line represents.

/Erik
> Emanuel
>   
>> --
>> 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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>   
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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys