[gmx-users] g_hbond

Erik Marklund erikm at xray.bmc.uu.se
Thu Oct 12 03:45:33 CEST 2006

Sounds like you you're using an old version of g_hbond. Either get a fresher 
version of gmx_hbond from the cvs repository or use g_hbond -nomerge. The 
latter generates unmerged hbn/hbm output that match. Look through the 


----- Original Message ----- 
From: "merc mertens" <merc.mertens at gmx.net>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, October 11, 2006 8:21 AM
Subject: [gmx-users] g_hbond


after using g_hbond to generate an *.xpm file one sees in the *.xpm file the 
following: "y-label: "Hydrogen Bond Index"" and the y-axis ranges between 0 
and 163. if i look in the additionally generated hbbond.ndx file, i see at 
the bottom of it the group "[ hbonds_* ]". i assumed that the number of 
lines with three atoms each in this group would correspond to the "hydrogen 
bond index" in the *.xpm file. but when i count the lines there are more 
than 164 (i.e. 180) in this group. does one line in "[ hbonds_* ]" not 
correspond to one hydrogen bond index? and if so, what else does it 
correspond to??

thanks for any help,
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