I think the confusion arises form 
15 aug 2012 kl. 22.53 skrev Justin Lemkul:

> 
> 
> On 8/15/12 4:49 PM, Andrew DeYoung wrote:
>> Hi,
>> 
>> 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
>> oooooo",
>> "
>> 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.
>> 
> 
> Your interpretation of the contents is correct.  The first entry in 
> hbonds.ndx is also the "first" entry in the .xpm file, which is the last line 
> (index zero, hence the first entry).  I have a script that calculates 
> hydrogen bond existence time (plot_hbmapl.pl) from these two files if you 
> want to confirm your outcome.
> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
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phone:    +46 18 471 6688        fax: +46 18 511 755
er...@xray.bmc.uu.se
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