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

Erik Marklund erikm at xray.bmc.uu.se
Fri Nov 30 13:33:11 CET 2012

30 nov 2012 kl. 12.24 skrev Cara Kreck:

> 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.

Thanks for pointing it out. I'd call it a bug, but a low priority one. Would you mind filing a redmine issue about it (http://redmine.gromacs.org/projects/gromacs/issues)? Then this will be much less likely to be overlooked or forgotten about.


> Cara
> 		 	   		  --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list