[gmx-developers] g_hbond

Francesco Oteri francesco.oteri at gmail.com
Wed Oct 6 21:43:31 CEST 2010

  Il 06/10/2010 16:03, Erik Marklund ha scritto:
>  Francesco Oteri skrev 2010-10-01 15.17:
>> Dear gromacs developers,
>> I will ask if is possible adding an option in g_hbond that to print, 
>> for each frame, the revealed hydrogen bond.
>> I think to something like:
>> time donors acceptors hbond_distance hbond_angle
>> Each time I change gromacs version, I heve to add this option to the 
>> code. Since is tedious but not difficult, I ask to developers to do 
>> this.
>> Having such a list makes easy monitoring each single h-bond with 
>> simple awk script without manipulating the .xpm file.
>> If you want, I can send you the code I wrote to print the list, using 
>> the 4.0.7 version
>> Francesco
> Hi,
> Would this really be information that can not be found in the -hbm and 
> -hbn output? If not, I would rather see a script that uses mentioned 
> files to produce the output you describe.
> Cheers,
Producing a list permits to better manage the informations (for example 
there is no file that displays the donor-acceptor distance, or the 
hydrogen bond angle).
Adding these abilities to g_hbond requires 20 line of code (more or 
less) so I don't find any good reason to don't produce such a list. 
Moreover this list should make easier extracting information regarding 
hydrogen bond: frequence, residence time, average distance and average 
The presence of a list, reduces the steps required to produce the 
previously described data, decreasing the frequence of error.

I think that writing a script only to convert the xpm should be useful 
if a lot of program will switch from xpm representation to flat list 

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