[gmx-users] g_hbond

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 10 15:59:28 CEST 2011

Justin A. Lemkul wrote:
> 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

Oops, forgot to finish that thought.  Someone came into my office...

Where I was going was that the code is very convoluted and I honestly can't 
follow it, so hopefully a developer can confirm the proper action so the 
documentation can be updated.


>> 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


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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