[gmx-users] Observations about g_hbond -dist and -ang

Cara Kreck cara_a_k at hotmail.com
Fri Nov 30 12:24:07 CET 2012

Hi everyone,

Ithought I should share something that I've noticed about some of the outputs of g_hbond, in case it's confused anyone else. I'd noticed that there is a significant difference in the length distribution plots (-dist)  produced by version 3.3.3 and all of the 4 family, including 4.5.5 (which I believe included a bugfix for g_hbond). I then figured out that this difference is really just a problem with the .xvg legends.

In 3.3.3 the distribution values were calculated for "Hydrogen - Acceptor Distance (nm)" and this description is still provided in the legend for 4.5.5, even though the values provided now are actually "Donor - Acceptor Distance (nm)". If you use -noda in 4.5.5 it will give you an identical distribution to 3.3.3. I then realised that both versions also have the angle distribution plots (-ang) labelled wrongly with "Donor - Hydrogen - Acceptor Angle (\SO\N)" instead of  "Hydrogen - Donor - Acceptor Angle". 

I'm not sure if these things would really be considered bugs, but I just thought I'd let people know.


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