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.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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