[gmx-users] g_hbond

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 10 15:57:21 CEST 2011

Mr Bernard Ramos wrote:
> Hi everyone!
> I have some questions on g_hbond. According to Manual 4.5.4, 
> hydrogen-bonds are counted/determined by g_hbond based on angle and 
> distance cut-offs. The distance cut-off is based on the acceptor-donor 
> distance. However, the online manual says that the distance is based on 
> Hydrogen - Acceptor distance? The link to the online manual is as follows: 
> http://manual.gromacs.org/online/g_hbond.html

It should be the donor-acceptor distance.  There was some discussion on this a 
few weeks ago.  The code

> I am using Gromacs 4.5.3. I found out that g_hbond does not give the 
> correct counts due to a bug
> http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html
> I am fairly new to using Gromacs with limited knowledge in programming. 
> How do I get this bug fixed with my current version? How can I patch the 
> fix suggested above?

I wouldn't bother.  That would require cherry-picking a commit from the git 
repository.  Just upgrade to the latest version of Gromacs and it will be fixed.

> The other question will be. Does the most recent version has the g_hbond 
> fixed? I use Gromacs via Cygwin. Just in case I install the the new 
> version, I would like to keep my old one. Is it ok, or do I have remove it?

You can maintain different versions concurrently as long as they are in discrete 
locations and you configure your environment to access the proper one (i.e. by 
sourcing the right GMXRC file).



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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