[gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond

Andrew DeYoung adeyoung at andrew.cmu.edu
Wed Aug 15 22:49:36 CEST 2012


I am a novice user of g_hbond (actually, I am using double precision --
g_hbond_d -- but I think all of the parameters should be the same).

I would like to use the output of the -hbn switch (which generates
hbond.ndx) in tandem with the -hbm switch (which generates an existence
matrix hbmap.xpm) to determine, using my own script, which hydrogen bonds
exist at each timestep in my trajectory.  My question is, how does the order
of entries in the [ hbonds ] section in hbond.ndx relate to the order of
entries in hbmap.xpm?

I am running Gromacs 4.5.5.  The man page for g_hbond_d clearly states:  

"-hbm:  existence matrix for all hydrogen bonds over all frames... .
Ordering is identical to that in -hbn index file."

However, I did a test of a system with two hydrogen bonds (which exist at
different times), and it seems (although I am not at all certain) that the
opposite is actually true.

My hbond.ndx file contains the following section at the end of the file:  

[ hbonds ]
    457    458    587
    457    458    737

And my hbmap.xpm file indeed contains two entries (following the enumeration
of x-axis values/times):

"ooooooooooooooo oooooooooooooooooooo oo oooo ooooooooooo
oooooooooooooooooooooooooooooooooo   o oooooooooooooooo ooo
oooooooooooooooooooooooooooooooooooooo ooooo ooo  oooooo  o oooooooo   ooooo
o o                       "

which tells me that one of the hydrogen bonds exists for a very large
fraction of the trajectory, whereas the other exists for only two timesteps
during the trajectory.

I visualized the system in VMD.  I clearly see that the hydrogen bond 457
458 737 (i.e., the _first_ entry in the [ hbonds ] section of the index
file) is the one that exists for the vast majority of the trajectory.
Conversely, the hydrogen bond 457 458 587 is clearly the one that exists for
only two timesteps in the trajectory.

Based on this, it seems that the top-to-bottom order of hbmap.xpm is
actually _opposite_ that of the [ hbonds ] section in hbond.ndx.

Has anyone else tested this?  If so, what conclusion did you reach about the
ordering in the -hbn and -hbm output files.  Or do you see a mistake in my
reasoning above?

One assumption I have made in my above reasoning is that "o" means "the
hydrogen bond exists", whereas " " means "the hydrogen bond does NOT exist".
I am not 100% sure that this is correct, but plotting the matrix as an EPS
file using xpm2ps seems to say that I am correct.

Thanks so much for your time.

Andrew DeYoung
Carnegie Mellon University

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