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