[gmx-developers] g_hbond

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 6 22:20:47 CEST 2010

Francesco Oteri wrote:
>  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 
> angle.
> The presence of a list, reduces the steps required to produce the 
> previously described data, decreasing the frequence of error.

If you have a code patch, I would suggest you upload it to the Bugzilla as an 
enhancement.  That way, the developers can assess the usefulness of the code and 
the potential for inclusion in a future release.


> 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 
> representation.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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