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
>>> 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
>> 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.
> 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.
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
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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