[gmx-users] Percentage of H-bonds

Oliver Grant olymacfoogal at gmail.com
Mon Oct 11 16:10:08 CEST 2010

Hi Carla,

I did this using g_hbond by supplying an index file with only the 3 atoms
involved in the individual bond I was looking at.

I got this printed to screen:

"Average number of hbonds per timeframe 0.998 out of 1 possible"

Although it is time consuming to do it for more than a few hydrogen bonds.


On 11 October 2010 14:49, Carla Jamous <carlajamous at gmail.com> wrote:

> Hi everyone,
> I tried to analyze the H-bonds in my trajectory with g-hbond and I analysed
> the xpm and ndx file. But now I need to know the percentage of existence of
> each hbond during my trajectory. Is there a way to do it with a command
> line? Or is there a program (someone told me there are python programs for
> analysis of gromacs trajectories) to extract this information from the .xpm
> file?
> Thank you.
> Cheers,
> Carla
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