[gmx-users] hbond correspondence between hbond.log and hbmap.xpm

Zheng Ruan zruan1991 at gmail.com
Wed Jun 25 22:04:47 CEST 2014


I'm new to gromacs and right now I'm trying to use g_hbond to analyze
my trajectory. Basically, I create two selections in .ndx file and try
to find hydrogen bonds between them. In the output, there is a
"y-axis" record in hbond.xpm matrix file. The number of the elements
of "y-axis" is the same with those in hbond.log file. I was wondering
if they referred to the same thing. That is, if the first row below
"y-axis" in hbmap.xpm telling me the hbond interaction of the first
interaction in hbond.log file? Or it's the reverse? I'm asking the
question because the hydrogen bond reported by g_hbond doesn't seems
to be consistent with those found by pymol.

Thank you!
Zheng Ruan

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